rs12050395

chr14-85744160-A-Gchr14-85744160-A-T

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 0.118 in 152,080 control chromosomes in the GnomAD database, including 1,778 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 0.12 (1778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17953 AN: 151964 Hom.: 1769 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.118 AC: 17989 AN: 152080 Hom.: 1778 Cov.: 32 AF XY: 0.125 AC XY: 9301 AN XY: 74326

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.0541

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0721 Hom.: 904

Bravo AF: 0.135

Asia WGS AF: 0.297 AC: 1031 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12050395; hg19: chr14-86210504;