rs10737175

Positions:

• chr1-159750152-T-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 0.253 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;