rs10494170

Variant names:

• chr1-115039096-G-A
• rs10494170

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 0.107 in 152,136 control chromosomes in the GnomAD database, including 1,630 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 0.11 (1630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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 (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.106 AC: 16164 AN: 152018 Hom.: 1621 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.107 AC: 16209 AN: 152136 Hom.: 1630 Cov.: 32 AF XY: 0.106 AC XY: 7897 AN XY: 74372

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.0505

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.0430

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0510 Hom.: 338

Bravo AF: 0.110

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494170; hg19: chr1-115581717;