rs12499618

Variant names:

• chr4-15935015-C-T
• rs12499618

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 0.0882 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0570

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.0974

Alfa AF: 0.0975 Hom.: 634

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12499618; hg19: chr4-15936638;