3-12695031-C-G

Variant names:

• chr3-12695031-C-G
• rs9818046

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 0.414 in 152,024 control chromosomes in the GnomAD database, including 14,125 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 0.41 (14125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 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: 0.414 AC: 62930 AN: 151906 Hom.: 14120 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.414 AC: 62967 AN: 152024 Hom.: 14125 Cov.: 32 AF XY: 0.422 AC XY: 31346 AN XY: 74320

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.404

Alfa AF: 0.265 Hom.: 680

Bravo AF: 0.402

Asia WGS AF: 0.700 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.083
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9818046; hg19: chr3-12736530;