15-63042566-G-A

Position:

• chr15-63042566-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The variant allele was found at a frequency of 0.0104 in 418,892 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.011 (26 hom., cov: 33)
  • Exomes 𝑓: 0.0099 (18 hom.)
• Consequence: intergenic_region
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0690

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP6: Variant 15-63042566-G-A is Benign according to our data. Variant chr15-63042566-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 674393.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63042566G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0111 AC: 1691 AN: 152068 Hom.: 26 Cov.: 33

Gnomad AFR AF: 0.00266

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.00908

GnomAD4 exome AF: 0.00993 AC: 2648 AN: 266714 Hom.: 18 AF XY: 0.00868 AC XY: 1262 AN XY: 145378

Gnomad4 AFR exome AF: 0.00166

Gnomad4 AMR exome AF: 0.00321

Gnomad4 ASJ exome AF: 0.00892

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000574

Gnomad4 FIN exome AF: 0.0302

Gnomad4 NFE exome AF: 0.0124

Gnomad4 OTH exome AF: 0.00988

GnomAD4 genome AF: 0.0111 AC: 1691 AN: 152178 Hom.: 26 Cov.: 33 AF XY: 0.0122 AC XY: 906 AN XY: 74402

Gnomad4 AFR AF: 0.00265

Gnomad4 AMR AF: 0.00301

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.00899

Alfa AF: 0.0106 Hom.: 1

Asia WGS AF: 0.00116 AC: 5 AN: 3474

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely 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	-0.53
CADD	Benign	15
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs528589173; hg19: chr15-63334765;