rs12499086

Variant names:

• chr4-105530154-G-A
• rs12499086

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 0.574 in 151,936 control chromosomes in the GnomAD database, including 27,396 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 0.57 (27396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 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: 0.575 AC: 87256 AN: 151818 Hom.: 27401 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.574 AC: 87249 AN: 151936 Hom.: 27396 Cov.: 31 AF XY: 0.567 AC XY: 42101 AN XY: 74282

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.591

Alfa AF: 0.691 Hom.: 26845

Bravo AF: 0.548

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12499086; hg19: chr4-106451311;