12-37463949-T-C

Variant names:

• chr12-37463949-T-C
• rs3956186

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 0.524 in 152,034 control chromosomes in the GnomAD database, including 22,411 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 0.52 (22411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79669 AN: 151916 Hom.: 22410 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.524 AC: 79695 AN: 152034 Hom.: 22411 Cov.: 32 AF XY: 0.526 AC XY: 39119 AN XY: 74304

African (AFR) AF: 0.311 AC: 12911 AN: 41490

American (AMR) AF: 0.569 AC: 8686 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2277 AN: 3466

East Asian (EAS) AF: 0.826 AC: 4263 AN: 5160

South Asian (SAS) AF: 0.641 AC: 3089 AN: 4820

European-Finnish (FIN) AF: 0.551 AC: 5808 AN: 10544

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40745 AN: 67970

Other (OTH) AF: 0.576 AC: 1217 AN: 2114

Alfa AF: 0.552 Hom.: 3735

Bravo AF: 0.513

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.9
DANN	Benign	0.79
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs3956186; hg19: chr12-37857751;