rs9710693

Variant names:

• chr2-238813613-T-C
• rs9710693

Your query was ambiguous. Multiple possible variants found:

• chr2-238813613-T-C
• chr2-238813613-T-G

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 0.645 in 151,960 control chromosomes in the GnomAD database, including 32,569 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 0.64 (32569 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.725 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: 0.645 AC: 97940 AN: 151842 Hom.: 32558 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.645 AC: 97996 AN: 151960 Hom.: 32569 Cov.: 31 AF XY: 0.637 AC XY: 47287 AN XY: 74246

African (AFR) AF: 0.579 AC: 24007 AN: 41460

American (AMR) AF: 0.564 AC: 8614 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2598 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1173 AN: 5132

South Asian (SAS) AF: 0.639 AC: 3072 AN: 4810

European-Finnish (FIN) AF: 0.625 AC: 6592 AN: 10552

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49612 AN: 67950

Other (OTH) AF: 0.678 AC: 1430 AN: 2108

Alfa AF: 0.705 Hom.: 73405

Bravo AF: 0.633

Asia WGS AF: 0.462 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9710693; hg19: chr2-239722254;