rs264943

Variant names:

• chr2-103682083-C-A
• rs264943

Your query was ambiguous. Multiple possible variants found:

• chr2-103682083-C-A
• chr2-103682083-C-G
• chr2-103682083-C-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 0.598 in 151,954 control chromosomes in the GnomAD database, including 27,896 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 0.60 (27896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -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 = 0.967 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: 0.598 AC: 90789 AN: 151834 Hom.: 27847 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.598 AC: 90892 AN: 151954 Hom.: 27896 Cov.: 32 AF XY: 0.602 AC XY: 44684 AN XY: 74256

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.562

Alfa AF: 0.535 Hom.: 37568

Bravo AF: 0.610

Asia WGS AF: 0.857 AC: 2979 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	0.18
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs264943; hg19: chr2-104298541; COSMIC: COSV60086675;