8-119788818-T-C

Position:

chr8-119788818-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_003184.4(TAF2):c.1655A>G(p.Tyr552Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

TAF2
NM_003184.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.27

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.21704128).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF2	NM_003184.4 link	c.1655A>G	p.Tyr552Cys	missense_variant	13/26	ENST00000378164.7	NP_003175.2	Q6P1X5B3KMD8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TAF2	ENST00000378164.7 link	c.1655A>G	p.Tyr552Cys	missense_variant	13/26	1	NM_003184.4	ENSP00000367406.2	Q6P1X5
TAF2	ENST00000686879.1 link	c.1655A>G	p.Tyr552Cys	missense_variant	13/27			ENSP00000509206.1	A0A8I5KV60
TAF2	ENST00000685235.1 link	c.1655A>G	p.Tyr552Cys	missense_variant	13/26			ENSP00000510174.1	A0A8I5QJR0
TAF2	ENST00000688645.1 link	c.1655A>G	p.Tyr552Cys	missense_variant	13/25			ENSP00000509978.1	A0A8I5KSY6
TAF2	ENST00000523904.2 link	c.1541A>G	p.Tyr514Cys	missense_variant	12/25	3		ENSP00000430832.2	H0YC37
TAF2	ENST00000690144.1 link	c.1655A>G	p.Tyr552Cys	missense_variant	13/26			ENSP00000510548.1	A0A8I5KUQ2
TAF2	ENST00000685202.1 link	n.1655A>G		non_coding_transcript_exon_variant	13/27			ENSP00000509214.1	A0A8I5QJD7
TAF2	ENST00000685503.1 link	n.*1047A>G		non_coding_transcript_exon_variant	13/26			ENSP00000509198.1	A0A8I5KXS3
TAF2	ENST00000685663.1 link	n.*1527A>G		non_coding_transcript_exon_variant	15/28			ENSP00000508988.1	A0A8I5KUD2
TAF2	ENST00000685684.1 link	n.*3122A>G		non_coding_transcript_exon_variant	12/25			ENSP00000509441.1	A0A8I5KY57
TAF2	ENST00000685824.1 link	n.*1356A>G		non_coding_transcript_exon_variant	11/24			ENSP00000510262.1	A0A8I5KU60
TAF2	ENST00000685876.1 link	n.*1373A>G		non_coding_transcript_exon_variant	14/27			ENSP00000510493.1	A0A8I5KUD2
TAF2	ENST00000685993.1 link	n.*1470A>G		non_coding_transcript_exon_variant	12/25			ENSP00000510102.1	A0A8I5KU60
TAF2	ENST00000686098.1 link	n.*300A>G		non_coding_transcript_exon_variant	12/25			ENSP00000509102.1	A0A8I5KXP3
TAF2	ENST00000688037.1 link	n.*1074A>G		non_coding_transcript_exon_variant	10/23			ENSP00000510169.1	A0A8I5KRI4
TAF2	ENST00000689164.1 link	n.*300A>G		non_coding_transcript_exon_variant	11/24			ENSP00000508729.1	A0A8I5KR26
TAF2	ENST00000689919.1 link	n.*1373A>G		non_coding_transcript_exon_variant	14/26			ENSP00000510768.1	A0A8I5KUD2
TAF2	ENST00000690808.1 link	n.*891A>G		non_coding_transcript_exon_variant	13/26			ENSP00000509791.1	A0A8I5KVC1
TAF2	ENST00000690922.1 link	n.*67A>G		non_coding_transcript_exon_variant	13/26			ENSP00000509498.1	A0A8I5KPW0
TAF2	ENST00000691847.1 link	n.*956A>G		non_coding_transcript_exon_variant	12/24			ENSP00000509663.1	A0A8I5QJJ6
TAF2	ENST00000691880.1 link	n.*1311A>G		non_coding_transcript_exon_variant	12/25			ENSP00000508515.1	A0A8I5KNG3
TAF2	ENST00000692518.1 link	n.*1356A>G		non_coding_transcript_exon_variant	11/25			ENSP00000508959.1	A0A8I5KU60
TAF2	ENST00000692707.1 link	n.*1523A>G		non_coding_transcript_exon_variant	15/28			ENSP00000509024.1	A0A8I5KUD2
TAF2	ENST00000692916.1 link	n.*1042A>G		non_coding_transcript_exon_variant	12/25			ENSP00000509603.1	A0A8I5QJI9
TAF2	ENST00000685503.1 link	n.*1047A>G		3_prime_UTR_variant	13/26			ENSP00000509198.1	A0A8I5KXS3
TAF2	ENST00000685663.1 link	n.*1527A>G		3_prime_UTR_variant	15/28			ENSP00000508988.1	A0A8I5KUD2
TAF2	ENST00000685684.1 link	n.*3122A>G		3_prime_UTR_variant	12/25			ENSP00000509441.1	A0A8I5KY57
TAF2	ENST00000685824.1 link	n.*1356A>G		3_prime_UTR_variant	11/24			ENSP00000510262.1	A0A8I5KU60
TAF2	ENST00000685876.1 link	n.*1373A>G		3_prime_UTR_variant	14/27			ENSP00000510493.1	A0A8I5KUD2
TAF2	ENST00000685993.1 link	n.*1470A>G		3_prime_UTR_variant	12/25			ENSP00000510102.1	A0A8I5KU60
TAF2	ENST00000686098.1 link	n.*300A>G		3_prime_UTR_variant	12/25			ENSP00000509102.1	A0A8I5KXP3
TAF2	ENST00000688037.1 link	n.*1074A>G		3_prime_UTR_variant	10/23			ENSP00000510169.1	A0A8I5KRI4
TAF2	ENST00000689164.1 link	n.*300A>G		3_prime_UTR_variant	11/24			ENSP00000508729.1	A0A8I5KR26
TAF2	ENST00000689919.1 link	n.*1373A>G		3_prime_UTR_variant	14/26			ENSP00000510768.1	A0A8I5KUD2
TAF2	ENST00000690808.1 link	n.*891A>G		3_prime_UTR_variant	13/26			ENSP00000509791.1	A0A8I5KVC1
TAF2	ENST00000690922.1 link	n.*67A>G		3_prime_UTR_variant	13/26			ENSP00000509498.1	A0A8I5KPW0
TAF2	ENST00000691847.1 link	n.*956A>G		3_prime_UTR_variant	12/24			ENSP00000509663.1	A0A8I5QJJ6
TAF2	ENST00000691880.1 link	n.*1311A>G		3_prime_UTR_variant	12/25			ENSP00000508515.1	A0A8I5KNG3
TAF2	ENST00000692518.1 link	n.*1356A>G		3_prime_UTR_variant	11/25			ENSP00000508959.1	A0A8I5KU60
TAF2	ENST00000692707.1 link	n.*1523A>G		3_prime_UTR_variant	15/28			ENSP00000509024.1	A0A8I5KUD2
TAF2	ENST00000692916.1 link	n.*1042A>G		3_prime_UTR_variant	12/25			ENSP00000509603.1	A0A8I5QJI9

Frequencies

GnomAD3 genomes

AF:

0.0000131

AC:

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000796

AC:

AN:

251358

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000342

AC:

AN:

1461554

Hom.:

Cov.:

AF XY:

0.00000550

AC XY:

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000270

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000131

AC:

AN:

152152

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000151

ExAC

AF:

0.00000824

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.12

BayesDel_noAF

Benign

-0.31

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.014

Eigen

Benign

-0.081

Eigen_PC

Benign

0.15

FATHMM_MKL

Uncertain

0.97

LIST_S2

Uncertain

0.97

M_CAP

Benign

0.025

MetaRNN

Benign

0.22

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.46

PrimateAI

Pathogenic

0.91

PROVEAN

Benign

-1.4

REVEL

Benign

0.13

Sift

Benign

0.17

Sift4G

Benign

0.19

Polyphen

0.015

Vest4

0.64

MutPred

0.38

Loss of phosphorylation at Y552 (P = 0.0401);

MVP

0.10

MPC

0.51

ClinPred

0.43

GERP RS

5.6

Varity_R

0.41

gMVP

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over