5-141273689-C-T

Variant names:

• chr5-141273689-C-T
• rs10044936
• ENST00000624699.1:n.129-9755G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000624699.1(TAF7):​n.129-9755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0455 in 152,150 control chromosomes in the GnomAD database, including 154 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 0.046 (154 hom., cov: 32)
• Consequence: TAF7 ENST00000624699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 3 publications found

Genes affected

TAF7 (HGNC:11541): (TATA-box binding protein associated factor 7) The intronless gene for this transcription coactivator is located between the protocadherin beta and gamma gene clusters on chromosome 5. The protein encoded by this gene is a component of the TFIID protein complex, a complex which binds to the TATA box in class II promoters and recruits RNA polymerase II and other factors. This particular subunit interacts with the largest TFIID subunit, as well as multiple transcription activators. The protein is required for transcription by promoters targeted by RNA polymerase II. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624699.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAF7	ENST00000624699.1	TSL:3	n.129-9755G>A		intron	N/A
	TAF7	ENST00000686518.1		n.76-13198G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6918 AN: 152032 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0460

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.0449

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0455 AC: 6923 AN: 152150 Hom.: 154 Cov.: 32 AF XY: 0.0455 AC XY: 3383 AN XY: 74400

African (AFR) AF: 0.0343 AC: 1422 AN: 41488

American (AMR) AF: 0.0420 AC: 642 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3468

East Asian (EAS) AF: 0.0399 AC: 206 AN: 5166

South Asian (SAS) AF: 0.0735 AC: 354 AN: 4818

European-Finnish (FIN) AF: 0.0460 AC: 487 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0488 AC: 3317 AN: 68012

Other (OTH) AF: 0.0445 AC: 94 AN: 2114

Alfa AF: 0.0460 Hom.: 199

Bravo AF: 0.0438

Asia WGS AF: 0.0550 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs10044936; hg19: chr5-140653258;