3-12695031-C-G

Variant names:

• chr3-12695031-C-G
• rs9818046

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.295 AC: 12228 AN: 41476

American (AMR) AF: 0.407 AC: 6203 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4512 AN: 5170

South Asian (SAS) AF: 0.724 AC: 3487 AN: 4818

European-Finnish (FIN) AF: 0.431 AC: 4554 AN: 10564

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29164 AN: 67970

Other (OTH) AF: 0.404 AC: 849 AN: 2104

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs9818046; hg19: chr3-12736530;