rs9967838

Variant names:

• chr2-27745587-A-C
• rs9967838

Your query was ambiguous. Multiple possible variants found:

• chr2-27745587-A-C
• chr2-27745587-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.624 in 150,606 control chromosomes in the GnomAD database, including 31,027 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 0.62 (31027 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 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: 0.624 AC: 93987 AN: 150532 Hom.: 31035 Cov.: 30

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.624 AC: 93989 AN: 150606 Hom.: 31027 Cov.: 30 AF XY: 0.622 AC XY: 45748 AN XY: 73544

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.650

Alfa AF: 0.654 Hom.: 4387

Bravo AF: 0.590

Asia WGS AF: 0.518 AC: 1799 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9967838; hg19: chr2-27968454;