rs12499086

chr4-105530154-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;