rs12441817

Variant names:

• chr15-74733473-T-C
• rs12441817

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 0.169 in 152,078 control chromosomes in the GnomAD database, including 3,200 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 0.17 (3200 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 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: 0.168 AC: 25566 AN: 151960 Hom.: 3178 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0821

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.169 AC: 25647 AN: 152078 Hom.: 3200 Cov.: 32 AF XY: 0.177 AC XY: 13182 AN XY: 74332

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.171

Alfa AF: 0.111 Hom.: 2440

Bravo AF: 0.184

Asia WGS AF: 0.452 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.13
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12441817; hg19: chr15-75025814;