chr12-114586432-A-G

Variant names:

• chr12-114586432-A-G
• rs1718377

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 0.866 in 152,080 control chromosomes in the GnomAD database, including 58,167 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 0.87 (58167 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.866 AC: 131581 AN: 151962 Hom.: 58123 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.866 AC: 131685 AN: 152080 Hom.: 58167 Cov.: 31 AF XY: 0.871 AC XY: 64743 AN XY: 74364

African (AFR) AF: 0.666 AC: 27570 AN: 41402

American (AMR) AF: 0.933 AC: 14248 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3178 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5164

South Asian (SAS) AF: 0.930 AC: 4489 AN: 4826

European-Finnish (FIN) AF: 0.966 AC: 10252 AN: 10616

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63749 AN: 68020

Other (OTH) AF: 0.899 AC: 1897 AN: 2110

Alfa AF: 0.915 Hom.: 109973

Bravo AF: 0.855

Asia WGS AF: 0.950 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.5
DANN	Benign	0.84
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1718377; hg19: chr12-115024237;