Variant chr1-229602423-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014409.4(TAF5L):c.744A>C(p.Arg248Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 1,613,782 control chromosomes in the GnomAD database, including 227,411 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22008 hom., cov: 31)

Exomes 𝑓: 0.53 ( 205403 hom. )

Consequence

TAF5L
NM_014409.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.83

Variant links:

Genes affected

TAF5L (HGNC:17304): (TATA-box binding protein associated factor 5 like) The product of this gene belongs to the WD-repeat TAF5 family of proteins. This gene encodes a protein that is a component of the PCAF histone acetylase complex. The PCAF histone acetylase complex, which is composed of more than 20 polypeptides some of which are TAFs, is required for myogenic transcription and differentiation. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors to facilitate complex assembly and transcription initiation. The encoded protein is structurally similar to one of the histone-like TAFs, TAF5. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

TAF5L links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP7

Synonymous conserved (PhyloP=-4.83 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAF5L	NM_014409.4 linkuse as main transcript	c.744A>C	p.Arg248Arg	synonymous_variant	4/5	ENST00000258281.7	NP_055224.1	O75529-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAF5L	ENST00000258281.7 linkuse as main transcript	c.744A>C	p.Arg248Arg	synonymous_variant	4/5	5	NM_014409.4	ENSP00000258281.2		O75529-1
TAF5L	ENST00000366675.3 linkuse as main transcript	c.744A>C	p.Arg248Arg	synonymous_variant	4/4	1		ENSP00000355635.3		O75529-2

Frequencies

GnomAD3 genomes

AF:

0.535

AC:

81218

AN:

151812

Hom.:

21982

Cov.:

show subpopulations

Gnomad AFR

AF:

0.513

Gnomad AMI

AF:

0.461

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.767

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.568

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.514

Gnomad OTH

AF:

0.529

GnomAD3 exomes

AF:

0.560

AC:

140559

AN:

251022

Hom.:

40288

AF XY:

0.554

AC XY:

75180

AN XY:

135664

show subpopulations

Gnomad AFR exome

AF:

0.513

Gnomad AMR exome

AF:

0.665

Gnomad ASJ exome

AF:

0.488

Gnomad EAS exome

AF:

0.757

Gnomad SAS exome

AF:

0.553

Gnomad FIN exome

AF:

0.567

Gnomad NFE exome

AF:

0.511

Gnomad OTH exome

AF:

0.545

GnomAD4 exome

AF:

0.527

AC:

769932

AN:

1461852

Hom.:

205403

Cov.:

AF XY:

0.527

AC XY:

383593

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.511

Gnomad4 AMR exome

AF:

0.652

Gnomad4 ASJ exome

AF:

0.489

Gnomad4 EAS exome

AF:

0.800

Gnomad4 SAS exome

AF:

0.553

Gnomad4 FIN exome

AF:

0.558

Gnomad4 NFE exome

AF:

0.509

Gnomad4 OTH exome

AF:

0.532

GnomAD4 genome

AF:

0.535

AC:

81301

AN:

151930

Hom.:

22008

Cov.:

AF XY:

0.544

AC XY:

40426

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.513

Gnomad4 AMR

AF:

0.591

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.768

Gnomad4 SAS

AF:

0.568

Gnomad4 FIN

AF:

0.568

Gnomad4 NFE

AF:

0.514

Gnomad4 OTH

AF:

0.529

Alfa

AF:

0.508

Hom.:

17977

Bravo

AF:

0.535

Asia WGS

AF:

0.632

AC:

2194

AN:

3478

EpiCase

AF:

0.516

EpiControl

AF:

0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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