rs9917256

Variant names:

• chr2-168286525-G-A
• rs9917256

Your query was ambiguous. Multiple possible variants found:

• chr2-168286525-G-A
• chr2-168286525-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 0.136 in 152,112 control chromosomes in the GnomAD database, including 1,617 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 (1617 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 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: 0.136 AC: 20732 AN: 151994 Hom.: 1616 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.0913

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.136 AC: 20740 AN: 152112 Hom.: 1617 Cov.: 31 AF XY: 0.139 AC XY: 10303 AN XY: 74350

African (AFR) AF: 0.104 AC: 4325 AN: 41488

American (AMR) AF: 0.196 AC: 2995 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0913 AC: 317 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1614 AN: 5168

South Asian (SAS) AF: 0.186 AC: 898 AN: 4818

European-Finnish (FIN) AF: 0.160 AC: 1693 AN: 10572

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.125 AC: 8467 AN: 68006

Other (OTH) AF: 0.148 AC: 312 AN: 2112

Alfa AF: 0.127 Hom.: 4690

Bravo AF: 0.139

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.75
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs9917256; hg19: chr2-169143035;