rs17157663

Variant names:

• chr7-8959346-G-A
• rs17157663

Your query was ambiguous. Multiple possible variants found:

• chr7-8959346-G-A
• chr7-8959346-G-T

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 0.208 in 152,048 control chromosomes in the GnomAD database, including 3,775 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 0.21 (3775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 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: 0.208 AC: 31627 AN: 151930 Hom.: 3769 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.208 AC: 31641 AN: 152048 Hom.: 3775 Cov.: 32 AF XY: 0.212 AC XY: 15728 AN XY: 74342

African (AFR) AF: 0.112 AC: 4655 AN: 41502

American (AMR) AF: 0.317 AC: 4840 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3466

East Asian (EAS) AF: 0.159 AC: 824 AN: 5182

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4826

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10568

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15762 AN: 67912

Other (OTH) AF: 0.212 AC: 448 AN: 2110

Alfa AF: 0.222 Hom.: 8566

Bravo AF: 0.207

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.30
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs17157663; hg19: chr7-8998976;