15-62121815-C-T

Variant names:

• chr15-62121815-C-T
• rs1436953

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 0.595 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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.710 AC: 29362 AN: 41370

American (AMR) AF: 0.562 AC: 8578 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1731 AN: 5146

South Asian (SAS) AF: 0.449 AC: 2147 AN: 4784

European-Finnish (FIN) AF: 0.575 AC: 6066 AN: 10542

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38634 AN: 67924

Other (OTH) AF: 0.600 AC: 1262 AN: 2104

Alfa AF: 0.575 Hom.: 99789

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1436953; hg19: chr15-62414014;