rs2413914

Variant names:

• chr15-48812311-C-T
• rs2413914

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 0.831 in 152,174 control chromosomes in the GnomAD database, including 53,190 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 0.83 (53190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.831 AC: 126409 AN: 152058 Hom.: 53142 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.831 AC: 126513 AN: 152174 Hom.: 53190 Cov.: 32 AF XY: 0.836 AC XY: 62202 AN XY: 74396

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.864

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.852

Alfa AF: 0.862 Hom.: 25770

Bravo AF: 0.828

Asia WGS AF: 0.948 AC: 3298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.13
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2413914; hg19: chr15-49104508;