Variant chr10-7964581-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_031923.4(TAF3):c.1071C>T(p.Ile357=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00936 in 1,614,012 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0072 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0096 ( 92 hom. )

Consequence

TAF3
NM_031923.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.547

Variant links:

Genes affected

TAF3 (HGNC:17303): (TATA-box binding protein associated factor 3) The highly conserved RNA polymerase II transcription factor TFIID (see TAF1; MIM 313650) comprises the TATA box-binding protein (TBP; MIM 600075) and a set of TBP-associated factors (TAFs), including TAF3. TAFs contribute to promoter recognition and selectivity and act as antiapoptotic factors (Gangloff et al., 2001 [PubMed 11438666]).[supplied by OMIM, May 2009]

TAF3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 10-7964581-C-T is Benign according to our data. Variant chr10-7964581-C-T is described in ClinVar as [Benign]. Clinvar id is 778458.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.547 with no splicing effect.

BS2

High AC in GnomAd4 at 1102 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAF3	NM_031923.4 linkuse as main transcript	c.1071C>T	p.Ile357=	synonymous_variant	3/7	ENST00000344293.6
TAF3	XM_011519741.2 linkuse as main transcript	c.1068C>T	p.Ile356=	synonymous_variant	3/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAF3	ENST00000344293.6 linkuse as main transcript	c.1071C>T	p.Ile357=	synonymous_variant	3/7	1	NM_031923.4	P4

Frequencies

GnomAD3 genomes

AF:

0.00726

AC:

1104

AN:

152068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00162

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00543

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0166

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0108

Gnomad OTH

AF:

0.00670

GnomAD3 exomes

AF:

0.00750

AC:

1866

AN:

248788

Hom.:

AF XY:

0.00779

AC XY:

1052

AN XY:

135016

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00406

Gnomad ASJ exome

AF:

0.00339

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00301

Gnomad FIN exome

AF:

0.0167

Gnomad NFE exome

AF:

0.0104

Gnomad OTH exome

AF:

0.00745

GnomAD4 exome

AF:

0.00958

AC:

14009

AN:

1461826

Hom.:

Cov.:

AF XY:

0.00936

AC XY:

6807

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.00185

Gnomad4 AMR exome

AF:

0.00452

Gnomad4 ASJ exome

AF:

0.00356

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00319

Gnomad4 FIN exome

AF:

0.0186

Gnomad4 NFE exome

AF:

0.0106

Gnomad4 OTH exome

AF:

0.00853

GnomAD4 genome

AF:

0.00724

AC:

1102

AN:

152186

Hom.:

Cov.:

AF XY:

0.00722

AC XY:

537

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.00161

Gnomad4 AMR

AF:

0.00543

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.0166

Gnomad4 NFE

AF:

0.0108

Gnomad4 OTH

AF:

0.00616

Alfa

AF:

0.00829

Hom.:

Bravo

AF:

0.00613

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.24

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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