rs2967340

Variant names:

• chr16-82223946-G-A
• rs2967340

Your query was ambiguous. Multiple possible variants found:

• chr16-82223946-G-A
• chr16-82223946-G-C

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 0.626 in 152,062 control chromosomes in the GnomAD database, including 35,618 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 0.63 (35618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

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 = 0.852 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: 0.626 AC: 95189 AN: 151944 Hom.: 35613 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.626 AC: 95191 AN: 152062 Hom.: 35618 Cov.: 32 AF XY: 0.620 AC XY: 46086 AN XY: 74320

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.676

Alfa AF: 0.810 Hom.: 89363

Bravo AF: 0.594

Asia WGS AF: 0.564 AC: 1961 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	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2967340; hg19: chr16-82257551;