ENST00000701867.2:n.57T>G

Variant names:

• chr5-141320922-T-G
• rs10875595
• ENST00000701867.2:n.57T>G

Variant summary

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

The ENST00000701867.2(ENSG00000288095):​n.57T>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 ENST00000701867.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701867.2. 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
	TAF7	NM_005642.3	MANE Select	c.-878A>C		upstream_gene	N/A	NP_005633.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288095	ENST00000701867.2		n.57T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000288095	ENST00000718184.1		n.56T>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000288095	ENST00000718185.1		n.33T>G		non_coding_transcript_exon	Exon 1 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 837 AN: 5004

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.235 AC: 8 AN: 34

Other (OTH) AF: 0.192 AC: 5 AN: 26

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

African (AFR) AF: 0.106 AC: 4410 AN: 41584

American (AMR) AF: 0.107 AC: 1631 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3472

East Asian (EAS) AF: 0.0670 AC: 348 AN: 5192

South Asian (SAS) AF: 0.113 AC: 548 AN: 4834

European-Finnish (FIN) AF: 0.177 AC: 1883 AN: 10622

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11925 AN: 68014

Other (OTH) AF: 0.132 AC: 279 AN: 2116

Alfa AF: 0.153 Hom.: 4602

Bravo AF: 0.133

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-2.5
PromoterAI		0.074	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10875595; hg19: chr5-140700489;