15-63042436-C-G

Position:

• chr15-63042436-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.12 in 151,922 control chromosomes in the GnomAD database, including 1,492 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1492 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.675

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 15-63042436-C-G is Benign according to our data. Variant chr15-63042436-C-G is described in ClinVar as [Benign]. Clinvar id is 668729.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 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: 0.120 AC: 18260 AN: 151808 Hom.: 1483 Cov.: 33

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0621

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.120 AC: 18287 AN: 151922 Hom.: 1492 Cov.: 33 AF XY: 0.127 AC XY: 9467 AN XY: 74286

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0796

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0608 Hom.: 58

Bravo AF: 0.116

Asia WGS AF: 0.370 AC: 1280 AN: 3470

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3825973; hg19: chr15-63334635;