3-9748794-G-A

Position:

• chr3-9748794-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;