rs10493150

Variant names:

• chr1-50329935-A-G
• rs10493150

Your query was ambiguous. Multiple possible variants found:

• chr1-50329935-A-G
• chr1-50329935-A-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 0.451 in 152,142 control chromosomes in the GnomAD database, including 16,021 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 0.45 (16021 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.451 AC: 68531 AN: 152022 Hom.: 15991 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.451 AC: 68607 AN: 152142 Hom.: 16021 Cov.: 33 AF XY: 0.444 AC XY: 33015 AN XY: 74356

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.483

Alfa AF: 0.446 Hom.: 1895

Bravo AF: 0.451

Asia WGS AF: 0.304 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493150; hg19: chr1-50795607;