3-186831295-G-A

Variant names:

• chr3-186831295-G-A
• rs12631446

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 0.362 in 151,800 control chromosomes in the GnomAD database, including 10,481 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 0.36 (10481 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 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: 0.362 AC: 54877 AN: 151682 Hom.: 10474 Cov.: 31

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.362 AC: 54918 AN: 151800 Hom.: 10481 Cov.: 31 AF XY: 0.372 AC XY: 27551 AN XY: 74140

African (AFR) AF: 0.303 AC: 12506 AN: 41338

American (AMR) AF: 0.419 AC: 6400 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2269 AN: 5130

South Asian (SAS) AF: 0.361 AC: 1737 AN: 4806

European-Finnish (FIN) AF: 0.555 AC: 5841 AN: 10518

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.348 AC: 23623 AN: 67962

Other (OTH) AF: 0.346 AC: 730 AN: 2112

Alfa AF: 0.230 Hom.: 560

Bravo AF: 0.350

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12631446; hg19: chr3-186549084;