rs125701

Variant names:

• chr3-9748794-G-A
• rs125701

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 0.126 in 152,332 control chromosomes in the GnomAD database, including 1,583 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 0.13 (1583 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.126 AC: 19181 AN: 152214 Hom.: 1584 Cov.: 33

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0971

Gnomad EAS AF: 0.0337

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.126 AC: 19178 AN: 152332 Hom.: 1583 Cov.: 33 AF XY: 0.127 AC XY: 9469 AN XY: 74490

Gnomad4 AFR AF: 0.0449

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0971

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.117

Alfa AF: 0.158 Hom.: 1302

Bravo AF: 0.111

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs125701; hg19: chr3-9790478;