rs12442098

chr15-97041640-C-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 0.084 in 151,502 control chromosomes in the GnomAD database, including 756 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 0.084 (756 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 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: 0.0840 AC: 12712 AN: 151392 Hom.: 752 Cov.: 32

Gnomad AFR AF: 0.0230

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0840 AC: 12724 AN: 151502 Hom.: 756 Cov.: 32 AF XY: 0.0867 AC XY: 6415 AN XY: 74026

Gnomad4 AFR AF: 0.0229

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.0959

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0954

Gnomad4 NFE AF: 0.0949

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.0945 Hom.: 303

Bravo AF: 0.0859

Asia WGS AF: 0.121 AC: 416 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.38
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12442098; hg19: chr15-97584870;