rs2295625

Variant names:

• chr1-229594705-G-A
• rs2295625
• NM_014409.4:c.1362C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-229594705-G-A
• chr1-229594705-G-C
• chr1-229594705-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_014409.4(TAF5L):​c.1362C>T​(p.Ser454Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 1,613,918 control chromosomes in the GnomAD database, including 156,422 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 0.36 (11204 hom., cov: 32)
  • Exomes 𝑓: 0.44 (145218 hom.)
• Consequence: TAF5L NM_014409.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 23 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP7: Synonymous conserved (PhyloP=0.139 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF5L	NM_014409.4	c.1362C>T	p.Ser454Ser	synonymous_variant	Exon 5 of 5	ENST00000258281.7	NP_055224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAF5L	ENST00000258281.7	c.1362C>T	p.Ser454Ser	synonymous_variant	Exon 5 of 5	5	NM_014409.4	ENSP00000258281.2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54156 AN: 151944 Hom.: 11203 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.377

GnomAD2 exomes AF: 0.397 AC: 99747 AN: 251242 AF XY: 0.408

Gnomad AFR exome AF: 0.131

Gnomad AMR exome AF: 0.262

Gnomad ASJ exome AF: 0.417

Gnomad EAS exome AF: 0.323

Gnomad FIN exome AF: 0.465

Gnomad NFE exome AF: 0.467

Gnomad OTH exome AF: 0.423

GnomAD4 exome AF: 0.440 AC: 643821 AN: 1461856 Hom.: 145218 Cov.: 94 AF XY: 0.442 AC XY: 321583 AN XY: 727226

African (AFR) AF: 0.129 AC: 4320 AN: 33480

American (AMR) AF: 0.265 AC: 11840 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 10850 AN: 26136

East Asian (EAS) AF: 0.317 AC: 12598 AN: 39700

South Asian (SAS) AF: 0.414 AC: 35672 AN: 86258

European-Finnish (FIN) AF: 0.462 AC: 24685 AN: 53386

Middle Eastern (MID) AF: 0.437 AC: 2522 AN: 5768

European-Non Finnish (NFE) AF: 0.464 AC: 516002 AN: 1112010

Other (OTH) AF: 0.419 AC: 25332 AN: 60394

GnomAD4 genome AF: 0.356 AC: 54174 AN: 152062 Hom.: 11204 Cov.: 32 AF XY: 0.358 AC XY: 26598 AN XY: 74320

African (AFR) AF: 0.143 AC: 5914 AN: 41494

American (AMR) AF: 0.311 AC: 4745 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1744 AN: 5152

South Asian (SAS) AF: 0.417 AC: 2008 AN: 4818

European-Finnish (FIN) AF: 0.463 AC: 4887 AN: 10554

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32085 AN: 67980

Other (OTH) AF: 0.380 AC: 802 AN: 2112

Alfa AF: 0.431 Hom.: 29342

Bravo AF: 0.330

Asia WGS AF: 0.359 AC: 1247 AN: 3478

EpiCase AF: 0.468

EpiControl AF: 0.465

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.99
DANN	Benign	0.59
PhyloP100		0.14
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Mutation Taster		=98/2	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2295625; hg19: chr1-229730452; COSMIC: COSV51080363; COSMIC: COSV51080363;