rs3809567

Variant names:

• chr15-63042321-C-A
• rs3809567

Your query was ambiguous. Multiple possible variants found:

• chr15-63042321-C-A
• chr15-63042321-C-T

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 0.122 in 152,230 control chromosomes in the GnomAD database, including 1,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1521 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0560

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP6: Variant 15-63042321-C-A is Benign according to our data. Variant chr15-63042321-C-A is described in ClinVar as [Benign]. Clinvar id is 668727.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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18576 AN: 152112 Hom.: 1512 Cov.: 33

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0795

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.122 AC: 18608 AN: 152230 Hom.: 1521 Cov.: 33 AF XY: 0.129 AC XY: 9604 AN XY: 74430

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0795

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0616 Hom.: 58

Bravo AF: 0.119

Asia WGS AF: 0.374 AC: 1297 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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	-0.72
CADD	Benign	7.3
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809567; hg19: chr15-63334520;