rs1436953

chr15-62121815-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 0.595 in 151,806 control chromosomes in the GnomAD database, including 27,362 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 0.60 (27362 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90245 AN: 151688 Hom.: 27299 Cov.: 29

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.595 AC: 90371 AN: 151806 Hom.: 27362 Cov.: 29 AF XY: 0.590 AC XY: 43754 AN XY: 74192

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.600

Alfa AF: 0.568 Hom.: 38789

Bravo AF: 0.598

Asia WGS AF: 0.462 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.97
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1436953; hg19: chr15-62414014;