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. The variant received -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
• Publications: 13 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 = 0.967 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.662 AC: 27433 AN: 41422

American (AMR) AF: 0.634 AC: 9669 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1868 AN: 3470

East Asian (EAS) AF: 0.990 AC: 5097 AN: 5148

South Asian (SAS) AF: 0.759 AC: 3656 AN: 4820

European-Finnish (FIN) AF: 0.523 AC: 5525 AN: 10558

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35840 AN: 67970

Other (OTH) AF: 0.562 AC: 1182 AN: 2102

Alfa AF: 0.548 Hom.: 64088

Bravo AF: 0.610

Asia WGS AF: 0.857 AC: 2979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.18
DANN	Benign	0.25
PhyloP100		0.11

Splicing

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

Other links and lift over

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