rs946263

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;