15-63042410-C-G

Position:

• chr15-63042410-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 0.123 in 152,224 control chromosomes in the GnomAD database, including 1,569 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1569 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 15-63042410-C-G is Benign according to our data. Variant chr15-63042410-C-G is described in ClinVar as [Benign]. Clinvar id is 668728.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.123 AC: 18696 AN: 152106 Hom.: 1560 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.123 AC: 18725 AN: 152224 Hom.: 1569 Cov.: 33 AF XY: 0.130 AC XY: 9671 AN XY: 74418

Gnomad4 AFR AF: 0.0847

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.125

Alfa AF: 0.0654 Hom.: 67

Bravo AF: 0.120

Asia WGS AF: 0.379 AC: 1310 AN: 3466

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	-0.83
CADD	Benign	6.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809568; hg19: chr15-63334609;