rs12499618

Variant names:

• chr4-15935015-C-T
• rs12499618

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 0.0882 in 152,268 control chromosomes in the GnomAD database, including 895 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 0.088 (895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 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: 0.0883 AC: 13435 AN: 152150 Hom.: 897 Cov.: 32

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0570

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0882 AC: 13429 AN: 152268 Hom.: 895 Cov.: 32 AF XY: 0.0902 AC XY: 6718 AN XY: 74452

African (AFR) AF: 0.0280 AC: 1164 AN: 41548

American (AMR) AF: 0.183 AC: 2798 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3472

East Asian (EAS) AF: 0.189 AC: 980 AN: 5178

South Asian (SAS) AF: 0.153 AC: 739 AN: 4828

European-Finnish (FIN) AF: 0.0570 AC: 605 AN: 10608

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6413 AN: 68034

Other (OTH) AF: 0.0974 AC: 206 AN: 2114

Alfa AF: 0.0958 Hom.: 816

Bravo AF: 0.0918

Asia WGS AF: 0.183 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.52
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs12499618; hg19: chr4-15936638;