rs10875595

Variant names:

• chr5-141320922-T-G
• rs10875595
• ENST00000701867.1:n.13T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701867.1(ENSG00000288095):​n.13T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 157,418 control chromosomes in the GnomAD database, including 1,745 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 0.14 (1672 hom., cov: 33)
  • Exomes 𝑓: 0.17 (73 hom.)
• Consequence: ENSG00000288095 ENST00000701867.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

ENSG00000288095 (HGNC:):

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAF7	NM_005642.3	c.-878A>C		upstream_gene_variant		ENST00000313368.8	NP_005633.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288095	ENST00000701867.1	n.13T>G		non_coding_transcript_exon_variant	Exon 1 of 2
TAF7	ENST00000313368.8	c.-878A>C		upstream_gene_variant		6	NM_005642.3	ENSP00000312709.5
TAF7	ENST00000624761.2	c.-599A>C		upstream_gene_variant		4		ENSP00000485510.2
ENSG00000288095	ENST00000670972.1	n.-58T>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21543 AN: 152230 Hom.: 1671 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.132

GnomAD4 exome AF: 0.168 AC: 850 AN: 5070 Hom.: 73 AF XY: 0.172 AC XY: 437 AN XY: 2544

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.192

GnomAD4 genome AF: 0.141 AC: 21548 AN: 152348 Hom.: 1672 Cov.: 33 AF XY: 0.140 AC XY: 10419 AN XY: 74500

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.132

Alfa AF: 0.159 Hom.: 2509

Bravo AF: 0.133

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10875595; hg19: chr5-140700489;