chr15-50374243-T-C

Variant names:

• chr15-50374243-T-C
• rs2414049

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 0.672 in 152,038 control chromosomes in the GnomAD database, including 34,835 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 0.67 (34835 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 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: 0.672 AC: 102061 AN: 151920 Hom.: 34814 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.672 AC: 102129 AN: 152038 Hom.: 34835 Cov.: 32 AF XY: 0.681 AC XY: 50586 AN XY: 74318

African (AFR) AF: 0.692 AC: 28679 AN: 41462

American (AMR) AF: 0.636 AC: 9704 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5129 AN: 5174

South Asian (SAS) AF: 0.717 AC: 3454 AN: 4820

European-Finnish (FIN) AF: 0.779 AC: 8230 AN: 10566

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42458 AN: 67976

Other (OTH) AF: 0.670 AC: 1409 AN: 2104

Alfa AF: 0.637 Hom.: 97219

Bravo AF: 0.660

Asia WGS AF: 0.853 AC: 2962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.39
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2414049; hg19: chr15-50666440;