chr3-12446012-T-C

Variant names:

• chr3-12446012-T-C
• rs1186464

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 0.087 in 152,310 control chromosomes in the GnomAD database, including 692 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 0.087 (692 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 6 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 (AMR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0870 AC: 13243 AN: 152192 Hom.: 690 Cov.: 33

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.0870 AC: 13257 AN: 152310 Hom.: 692 Cov.: 33 AF XY: 0.0876 AC XY: 6520 AN XY: 74468

African (AFR) AF: 0.0406 AC: 1686 AN: 41574

American (AMR) AF: 0.123 AC: 1884 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 339 AN: 3472

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5180

South Asian (SAS) AF: 0.0770 AC: 372 AN: 4830

European-Finnish (FIN) AF: 0.0951 AC: 1010 AN: 10616

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7337 AN: 68022

Other (OTH) AF: 0.129 AC: 272 AN: 2116

Alfa AF: 0.104 Hom.: 1185

Bravo AF: 0.0872

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.62
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1186464; hg19: chr3-12487511;