rs946263

Variant names:

• chr1-203196253-G-A
• rs946263

Your query was ambiguous. Multiple possible variants found:

• chr1-203196253-G-A
• chr1-203196253-G-C
• chr1-203196253-G-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 0.866 in 152,228 control chromosomes in the GnomAD database, including 57,371 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 0.87 (57371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.866 AC: 131741 AN: 152112 Hom.: 57316 Cov.: 32

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.866 AC: 131853 AN: 152228 Hom.: 57371 Cov.: 32 AF XY: 0.868 AC XY: 64575 AN XY: 74402

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.879

Alfa AF: 0.842 Hom.: 34286

Bravo AF: 0.880

Asia WGS AF: 0.916 AC: 3181 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.057
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs946263; hg19: chr1-203165381;