rs12631446

Variant names:

• chr3-186831295-G-A
• rs12631446

Your query was ambiguous. Multiple possible variants found:

• chr3-186831295-G-A
• chr3-186831295-G-C

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 0.362 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.346

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12631446; hg19: chr3-186549084;