rs10493150

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;