8-119732146-C-T

Position:

chr8-119732146-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7

The NM_003184.4(TAF2):c.3378G>A(p.Ala1126Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)

Exomes 𝑓: 0.000016 ( 0 hom. )

Consequence

TAF2
NM_003184.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.732

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 Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 8-119732146-C-T is Benign according to our data. Variant chr8-119732146-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1609113.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.732 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF2	NM_003184.4 link	c.3378G>A	p.Ala1126Ala	synonymous_variant	26/26	ENST00000378164.7	NP_003175.2	Q6P1X5B3KMD8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TAF2	ENST00000378164.7 link	c.3378G>A	p.Ala1126Ala	synonymous_variant	26/26	1	NM_003184.4	ENSP00000367406.2	Q6P1X5
TAF2	ENST00000686879.1 link	c.3534G>A	p.Ala1178Ala	synonymous_variant	27/27			ENSP00000509206.1	A0A8I5KV60
TAF2	ENST00000685235.1 link	c.3423G>A	p.Ala1141Ala	synonymous_variant	26/26			ENSP00000510174.1	A0A8I5QJR0
TAF2	ENST00000688645.1 link	c.3267G>A	p.Ala1089Ala	synonymous_variant	25/25			ENSP00000509978.1	A0A8I5KSY6
TAF2	ENST00000523904.2 link	c.3264G>A	p.Ala1088Ala	synonymous_variant	25/25	3		ENSP00000430832.2	H0YC37
TAF2	ENST00000690144 link	c.*509G>A		3_prime_UTR_variant	26/26			ENSP00000510548.1	A0A8I5KUQ2
TAF2	ENST00000685202.1 link	n.*903G>A		non_coding_transcript_exon_variant	27/27			ENSP00000509214.1	A0A8I5QJD7
TAF2	ENST00000685503.1 link	n.*2770G>A		non_coding_transcript_exon_variant	26/26			ENSP00000509198.1	A0A8I5KXS3
TAF2	ENST00000685663.1 link	n.*3250G>A		non_coding_transcript_exon_variant	28/28			ENSP00000508988.1	A0A8I5KUD2
TAF2	ENST00000685684.1 link	n.*4845G>A		non_coding_transcript_exon_variant	25/25			ENSP00000509441.1	A0A8I5KY57
TAF2	ENST00000685824.1 link	n.*3079G>A		non_coding_transcript_exon_variant	24/24			ENSP00000510262.1	A0A8I5KU60
TAF2	ENST00000685876.1 link	n.*3096G>A		non_coding_transcript_exon_variant	27/27			ENSP00000510493.1	A0A8I5KUD2
TAF2	ENST00000685993.1 link	n.*3193G>A		non_coding_transcript_exon_variant	25/25			ENSP00000510102.1	A0A8I5KU60
TAF2	ENST00000686098.1 link	n.*2023G>A		non_coding_transcript_exon_variant	25/25			ENSP00000509102.1	A0A8I5KXP3
TAF2	ENST00000688037.1 link	n.*2797G>A		non_coding_transcript_exon_variant	23/23			ENSP00000510169.1	A0A8I5KRI4
TAF2	ENST00000689164.1 link	n.*3996G>A		non_coding_transcript_exon_variant	24/24			ENSP00000508729.1	A0A8I5KR26
TAF2	ENST00000689919.1 link	n.*2985G>A		non_coding_transcript_exon_variant	26/26			ENSP00000510768.1	A0A8I5KUD2
TAF2	ENST00000690808.1 link	n.*2614G>A		non_coding_transcript_exon_variant	26/26			ENSP00000509791.1	A0A8I5KVC1
TAF2	ENST00000690922.1 link	n.*1790G>A		non_coding_transcript_exon_variant	26/26			ENSP00000509498.1	A0A8I5KPW0
TAF2	ENST00000691880.1 link	n.*3034G>A		non_coding_transcript_exon_variant	25/25			ENSP00000508515.1	A0A8I5KNG3
TAF2	ENST00000692518.1 link	n.*3244G>A		non_coding_transcript_exon_variant	25/25			ENSP00000508959.1	A0A8I5KU60
TAF2	ENST00000692707.1 link	n.*3246G>A		non_coding_transcript_exon_variant	28/28			ENSP00000509024.1	A0A8I5KUD2
TAF2	ENST00000692916.1 link	n.*2765G>A		non_coding_transcript_exon_variant	25/25			ENSP00000509603.1	A0A8I5QJI9
TAF2	ENST00000685202.1 link	n.*903G>A		3_prime_UTR_variant	27/27			ENSP00000509214.1	A0A8I5QJD7
TAF2	ENST00000685503.1 link	n.*2770G>A		3_prime_UTR_variant	26/26			ENSP00000509198.1	A0A8I5KXS3
TAF2	ENST00000685663.1 link	n.*3250G>A		3_prime_UTR_variant	28/28			ENSP00000508988.1	A0A8I5KUD2
TAF2	ENST00000685684.1 link	n.*4845G>A		3_prime_UTR_variant	25/25			ENSP00000509441.1	A0A8I5KY57
TAF2	ENST00000685824.1 link	n.*3079G>A		3_prime_UTR_variant	24/24			ENSP00000510262.1	A0A8I5KU60
TAF2	ENST00000685876.1 link	n.*3096G>A		3_prime_UTR_variant	27/27			ENSP00000510493.1	A0A8I5KUD2
TAF2	ENST00000685993.1 link	n.*3193G>A		3_prime_UTR_variant	25/25			ENSP00000510102.1	A0A8I5KU60
TAF2	ENST00000686098.1 link	n.*2023G>A		3_prime_UTR_variant	25/25			ENSP00000509102.1	A0A8I5KXP3
TAF2	ENST00000688037.1 link	n.*2797G>A		3_prime_UTR_variant	23/23			ENSP00000510169.1	A0A8I5KRI4
TAF2	ENST00000689164.1 link	n.*3996G>A		3_prime_UTR_variant	24/24			ENSP00000508729.1	A0A8I5KR26
TAF2	ENST00000689919.1 link	n.*2985G>A		3_prime_UTR_variant	26/26			ENSP00000510768.1	A0A8I5KUD2
TAF2	ENST00000690808.1 link	n.*2614G>A		3_prime_UTR_variant	26/26			ENSP00000509791.1	A0A8I5KVC1
TAF2	ENST00000690922.1 link	n.*1790G>A		3_prime_UTR_variant	26/26			ENSP00000509498.1	A0A8I5KPW0
TAF2	ENST00000691880.1 link	n.*3034G>A		3_prime_UTR_variant	25/25			ENSP00000508515.1	A0A8I5KNG3
TAF2	ENST00000692518.1 link	n.*3244G>A		3_prime_UTR_variant	25/25			ENSP00000508959.1	A0A8I5KU60
TAF2	ENST00000692707.1 link	n.*3246G>A		3_prime_UTR_variant	28/28			ENSP00000509024.1	A0A8I5KUD2
TAF2	ENST00000692916.1 link	n.*2765G>A		3_prime_UTR_variant	25/25			ENSP00000509603.1	A0A8I5QJI9

Frequencies

GnomAD3 genomes

AF:

0.0000197

AC:

AN:

152106

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:

0.0000441

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000159

AC:

AN:

251256

Hom.:

AF XY:

0.0000295

AC XY:

AN XY:

135788

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000867

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000157

AC:

AN:

1461866

Hom.:

Cov.:

AF XY:

0.0000151

AC XY:

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000671

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000117

Gnomad4 OTH exome

AF:

0.0000331

GnomAD4 genome

AF:

0.0000197

AC:

AN:

152106

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74296

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:

0.0000441

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000189

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 24, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

1.5

DANN

Benign

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over