rs10917825

Variant names:

• chr1-163730402-G-A
• rs10917825

Your query was ambiguous. Multiple possible variants found:

• chr1-163730402-G-A
• chr1-163730402-G-C

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 0.408 in 152,032 control chromosomes in the GnomAD database, including 13,437 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 0.41 (13437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.408 AC: 61941 AN: 151914 Hom.: 13425 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.408 AC: 61989 AN: 152032 Hom.: 13437 Cov.: 32 AF XY: 0.416 AC XY: 30899 AN XY: 74290

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.398

Alfa AF: 0.414 Hom.: 3635

Bravo AF: 0.397

Asia WGS AF: 0.657 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10917825; hg19: chr1-163699639;