rs1186464

Variant names:

• chr3-12446012-T-C
• rs1186464

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 0.087 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0870 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

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0976

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.129

Alfa AF: 0.108 Hom.: 846

Bravo AF: 0.0872

Asia WGS AF: 0.139 AC: 483 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	7.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1186464; hg19: chr3-12487511;