chr15-48343856-T-C

Variant names:

• chr15-48343856-T-C
• rs12441867

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 0.697 in 152,038 control chromosomes in the GnomAD database, including 39,411 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 0.70 (39411 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

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 (NFE) allele frequency at 95% confidence interval = 0.83 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: 0.697 AC: 105945 AN: 151920 Hom.: 39422 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.697 AC: 105950 AN: 152038 Hom.: 39411 Cov.: 31 AF XY: 0.698 AC XY: 51863 AN XY: 74314

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.702

Alfa AF: 0.794 Hom.: 46448

Bravo AF: 0.675

Asia WGS AF: 0.554 AC: 1929 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	1.5
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: rs12441867; hg19: chr15-48636053;