rs10917686

Positions:

• chr1-161688700-C-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 0.155 in 152,034 control chromosomes in the GnomAD database, including 2,356 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 0.16 (2356 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23631 AN: 151916 Hom.: 2356 Cov.: 31

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.155 AC: 23641 AN: 152034 Hom.: 2356 Cov.: 31 AF XY: 0.155 AC XY: 11513 AN XY: 74316

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.00811

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.169

Alfa AF: 0.182 Hom.: 386

Bravo AF: 0.147

Asia WGS AF: 0.120 AC: 416 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10917686; hg19: chr1-161658490;