rs1344063

Variant names:

• chr2-20961673-T-C
• rs1344063

Your query was ambiguous. Multiple possible variants found:

• chr2-20961673-T-C
• chr2-20961673-T-G

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 0.546 in 152,162 control chromosomes in the GnomAD database, including 23,256 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 0.55 (23256 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 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: 0.546 AC: 83019 AN: 152042 Hom.: 23253 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.546 AC: 83049 AN: 152162 Hom.: 23256 Cov.: 33 AF XY: 0.548 AC XY: 40720 AN XY: 74374

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.564

Alfa AF: 0.576 Hom.: 37346

Bravo AF: 0.537

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.084
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344063; hg19: chr2-21184545;