rs10917688

Variant names:

• chr1-161688990-C-T
• rs10917688

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 0.156 in 152,140 control chromosomes in the GnomAD database, including 2,361 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 (2361 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23648 AN: 152022 Hom.: 2361 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: 0.00770

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.176

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: 0.156 AC: 23658 AN: 152140 Hom.: 2361 Cov.: 31 AF XY: 0.155 AC XY: 11526 AN XY: 74364

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.00772

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.169

Alfa AF: 0.183 Hom.: 521

Bravo AF: 0.147

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
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: rs10917688; hg19: chr1-161658780;