rs10493513

Variant names:

• chr1-72913906-G-A
• rs10493513

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.38 in 151,808 control chromosomes in the GnomAD database, including 13,375 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 0.38 (13375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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: 0.380 AC: 57705 AN: 151690 Hom.: 13385 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.380 AC: 57700 AN: 151808 Hom.: 13375 Cov.: 32 AF XY: 0.383 AC XY: 28434 AN XY: 74180

Gnomad4 AFR AF: 0.116 AC: 0.116118 AN: 0.116118

Gnomad4 AMR AF: 0.495 AC: 0.495133 AN: 0.495133

Gnomad4 ASJ AF: 0.484 AC: 0.483862 AN: 0.483862

Gnomad4 EAS AF: 0.171 AC: 0.171078 AN: 0.171078

Gnomad4 SAS AF: 0.382 AC: 0.381999 AN: 0.381999

Gnomad4 FIN AF: 0.552 AC: 0.551557 AN: 0.551557

Gnomad4 NFE AF: 0.498 AC: 0.497967 AN: 0.497967

Gnomad4 OTH AF: 0.382 AC: 0.382493 AN: 0.382493

Alfa AF: 0.428 Hom.: 2075

Bravo AF: 0.366

Asia WGS AF: 0.261 AC: 908 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493513; hg19: chr1-73379589;