rs149772375

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_003184.4(TAF2):c.1655A>T(p.Tyr552Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00243 in 1,613,806 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0019 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0025 ( 14 hom. )

Consequence

TAF2
NM_003184.4 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 6.27

Publications

5 publications found

Variant links:

Genes affected

TAF2 (HGNC:11536): (TATA-box binding protein associated factor 2) Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes one of the larger subunits of TFIID that is stably associated with the TFIID complex. It contributes to interactions at and downstream of the transcription initiation site, interactions that help determine transcription complex response to activators. [provided by RefSeq, Jul 2008]

TAF2 Gene-Disease associations (from GenCC):

microcephaly-thin corpus callosum-intellectual disability syndrome
Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

TAF2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008978754).

BP6

Variant 8-119788818-T-A is Benign according to our data. Variant chr8-119788818-T-A is described in ClinVar as Likely_benign. ClinVar VariationId is 436940.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF2	NM_003184.4 link	c.1655A>T	p.Tyr552Phe	missense_variant	Exon 13 of 26	ENST00000378164.7	NP_003175.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
TAF2	ENST00000378164.7 link	c.1655A>T	p.Tyr552Phe	missense_variant	Exon 13 of 26	1	NM_003184.4	ENSP00000367406.2
TAF2	ENST00000686879.1 link	c.1655A>T	p.Tyr552Phe	missense_variant	Exon 13 of 27			ENSP00000509206.1
TAF2	ENST00000685235.1 link	c.1655A>T	p.Tyr552Phe	missense_variant	Exon 13 of 26			ENSP00000510174.1
TAF2	ENST00000688645.1 link	c.1655A>T	p.Tyr552Phe	missense_variant	Exon 13 of 25			ENSP00000509978.1
TAF2	ENST00000523904.2 link	c.1541A>T	p.Tyr514Phe	missense_variant	Exon 12 of 25	3		ENSP00000430832.2
TAF2	ENST00000690144.1 link	c.1655A>T	p.Tyr552Phe	missense_variant	Exon 13 of 26			ENSP00000510548.1
TAF2	ENST00000685202.1 link	n.1655A>T		non_coding_transcript_exon_variant	Exon 13 of 27			ENSP00000509214.1
TAF2	ENST00000685503.1 link	n.*1047A>T		non_coding_transcript_exon_variant	Exon 13 of 26			ENSP00000509198.1
TAF2	ENST00000685663.1 link	n.*1527A>T		non_coding_transcript_exon_variant	Exon 15 of 28			ENSP00000508988.1
TAF2	ENST00000685684.1 link	n.*3122A>T		non_coding_transcript_exon_variant	Exon 12 of 25			ENSP00000509441.1
TAF2	ENST00000685824.1 link	n.*1356A>T		non_coding_transcript_exon_variant	Exon 11 of 24			ENSP00000510262.1
TAF2	ENST00000685876.1 link	n.*1373A>T		non_coding_transcript_exon_variant	Exon 14 of 27			ENSP00000510493.1
TAF2	ENST00000685993.1 link	n.*1470A>T		non_coding_transcript_exon_variant	Exon 12 of 25			ENSP00000510102.1
TAF2	ENST00000686098.1 link	n.*300A>T		non_coding_transcript_exon_variant	Exon 12 of 25			ENSP00000509102.1
TAF2	ENST00000688037.1 link	n.*1074A>T		non_coding_transcript_exon_variant	Exon 10 of 23			ENSP00000510169.1
TAF2	ENST00000689164.1 link	n.*300A>T		non_coding_transcript_exon_variant	Exon 11 of 24			ENSP00000508729.1
TAF2	ENST00000689919.1 link	n.*1373A>T		non_coding_transcript_exon_variant	Exon 14 of 26			ENSP00000510768.1
TAF2	ENST00000690808.1 link	n.*891A>T		non_coding_transcript_exon_variant	Exon 13 of 26			ENSP00000509791.1
TAF2	ENST00000690922.1 link	n.*67A>T		non_coding_transcript_exon_variant	Exon 13 of 26			ENSP00000509498.1
TAF2	ENST00000691847.1 link	n.*956A>T		non_coding_transcript_exon_variant	Exon 12 of 24			ENSP00000509663.1
TAF2	ENST00000691880.1 link	n.*1311A>T		non_coding_transcript_exon_variant	Exon 12 of 25			ENSP00000508515.1
TAF2	ENST00000692518.1 link	n.*1356A>T		non_coding_transcript_exon_variant	Exon 11 of 25			ENSP00000508959.1
TAF2	ENST00000692707.1 link	n.*1523A>T		non_coding_transcript_exon_variant	Exon 15 of 28			ENSP00000509024.1
TAF2	ENST00000692916.1 link	n.*1042A>T		non_coding_transcript_exon_variant	Exon 12 of 25			ENSP00000509603.1
TAF2	ENST00000685503.1 link	n.*1047A>T		3_prime_UTR_variant	Exon 13 of 26			ENSP00000509198.1
TAF2	ENST00000685663.1 link	n.*1527A>T		3_prime_UTR_variant	Exon 15 of 28			ENSP00000508988.1
TAF2	ENST00000685684.1 link	n.*3122A>T		3_prime_UTR_variant	Exon 12 of 25			ENSP00000509441.1
TAF2	ENST00000685824.1 link	n.*1356A>T		3_prime_UTR_variant	Exon 11 of 24			ENSP00000510262.1
TAF2	ENST00000685876.1 link	n.*1373A>T		3_prime_UTR_variant	Exon 14 of 27			ENSP00000510493.1
TAF2	ENST00000685993.1 link	n.*1470A>T		3_prime_UTR_variant	Exon 12 of 25			ENSP00000510102.1
TAF2	ENST00000686098.1 link	n.*300A>T		3_prime_UTR_variant	Exon 12 of 25			ENSP00000509102.1
TAF2	ENST00000688037.1 link	n.*1074A>T		3_prime_UTR_variant	Exon 10 of 23			ENSP00000510169.1
TAF2	ENST00000689164.1 link	n.*300A>T		3_prime_UTR_variant	Exon 11 of 24			ENSP00000508729.1
TAF2	ENST00000689919.1 link	n.*1373A>T		3_prime_UTR_variant	Exon 14 of 26			ENSP00000510768.1
TAF2	ENST00000690808.1 link	n.*891A>T		3_prime_UTR_variant	Exon 13 of 26			ENSP00000509791.1
TAF2	ENST00000690922.1 link	n.*67A>T		3_prime_UTR_variant	Exon 13 of 26			ENSP00000509498.1
TAF2	ENST00000691847.1 link	n.*956A>T		3_prime_UTR_variant	Exon 12 of 24			ENSP00000509663.1
TAF2	ENST00000691880.1 link	n.*1311A>T		3_prime_UTR_variant	Exon 12 of 25			ENSP00000508515.1
TAF2	ENST00000692518.1 link	n.*1356A>T		3_prime_UTR_variant	Exon 11 of 25			ENSP00000508959.1
TAF2	ENST00000692707.1 link	n.*1523A>T		3_prime_UTR_variant	Exon 15 of 28			ENSP00000509024.1
TAF2	ENST00000692916.1 link	n.*1042A>T		3_prime_UTR_variant	Exon 12 of 25			ENSP00000509603.1

Frequencies

GnomAD3 genomes

AF:

0.00188

AC:

286

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.00321

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00254

Gnomad OTH

AF:

0.00288

GnomAD2 exomes

AF:

0.00266

AC:

669

AN:

251358

AF XY:

0.00260

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.00572

Gnomad ASJ exome

AF:

0.00516

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000601

Gnomad NFE exome

AF:

0.00280

Gnomad OTH exome

AF:

0.00914

GnomAD4 exome

AF:

0.00249

AC:

3634

AN:

1461538

Hom.:

Cov.:

AF XY:

0.00251

AC XY:

1828

AN XY:

727096

show subpopulations

African (AFR)

AF:

0.000329

AC:

AN:

33474

American (AMR)

AF:

0.00601

AC:

269

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00742

AC:

194

AN:

26128

East Asian (EAS)

AF:

0.00

AC:

AN:

39656

South Asian (SAS)

AF:

0.000974

AC:

AN:

86252

European-Finnish (FIN)

AF:

0.000693

AC:

AN:

53416

Middle Eastern (MID)

AF:

0.00642

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00250

AC:

2783

AN:

1111742

Other (OTH)

AF:

0.00363

AC:

219

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

179

357

536

714

893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

204

306

408

510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00187

AC:

285

AN:

152268

Hom.:

Cov.:

AF XY:

0.00167

AC XY:

124

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.000337

AC:

AN:

41580

American (AMR)

AF:

0.00321

AC:

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00490

AC:

AN:

3468

East Asian (EAS)

AF:

0.000194

AC:

AN:

5160

South Asian (SAS)

AF:

0.00124

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.000282

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00253

AC:

172

AN:

68018

Other (OTH)

AF:

0.00285

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00240

Hom.:

Bravo

AF:

0.00237

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.00104

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.00302

AC:

ExAC

AF:

0.00259

AC:

314

Asia WGS

AF:

0.000578

AC:

AN:

3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Sep 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

TAF2: BS2

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

not specified

Benign:1

Aug 13, 2018

Genetic Services Laboratory, University of Chicago

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Microcephaly-thin corpus callosum-intellectual disability syndrome

Benign:1

Feb 10, 2022

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.38

BayesDel_noAF

Benign

-0.32

CADD

Benign

(source)

DANN

Benign

0.85

DEOGEN2

Benign

0.0099

Eigen

Benign

-0.18

Eigen_PC

Benign

0.062

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.95

M_CAP

Benign

0.014

MetaRNN

Benign

0.0090

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.0

PhyloP100

6.3

PrimateAI

Pathogenic

0.87

PROVEAN

Benign

-0.66

REVEL

Benign

0.15

Sift

Benign

0.67

Sift4G

Benign

0.68

Vest4

0.67

ClinPred

0.026

GERP RS

5.6

Varity_R

0.33

gMVP

0.35

Mutation Taster

=92/8

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over