chr15-85801681-C-T

Variant names:

• chr15-85801681-C-T
• rs7181017

Variant summary

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

The variant allele was found at a frequency of 0.134 in 151,898 control chromosomes in the GnomAD database, including 1,477 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 0.13 (1477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20293 AN: 151780 Hom.: 1477 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.134 AC: 20315 AN: 151898 Hom.: 1477 Cov.: 31 AF XY: 0.137 AC XY: 10178 AN XY: 74244

African (AFR) AF: 0.153 AC: 6315 AN: 41250

American (AMR) AF: 0.140 AC: 2139 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5178

South Asian (SAS) AF: 0.153 AC: 740 AN: 4828

European-Finnish (FIN) AF: 0.147 AC: 1557 AN: 10564

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7570 AN: 68012

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.120 Hom.: 5107

Bravo AF: 0.133

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.50
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7181017; hg19: chr15-86344912;