rs2413914

Positions:

• chr15-48812311-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 0.831 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;