rs10737175

Variant names:

• chr1-159750152-T-C
• rs10737175

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 0.253 in 152,134 control chromosomes in the GnomAD database, including 5,721 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 0.25 (5721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.253 AC: 38496 AN: 152016 Hom.: 5721 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.253 AC: 38502 AN: 152134 Hom.: 5721 Cov.: 32 AF XY: 0.255 AC XY: 18993 AN XY: 74386

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.285

Alfa AF: 0.252 Hom.: 1019

Bravo AF: 0.255

Asia WGS AF: 0.495 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10737175; hg19: chr1-159719942;