rs16787

chr15-55508639-G-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 0.826 in 152,188 control chromosomes in the GnomAD database, including 52,878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.83 (52878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 15-55508639-G-T is Benign according to our data. Variant chr15-55508639-G-T is described in ClinVar as [Benign]. Clinvar id is 1168573.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125646 AN: 152070 Hom.: 52822 Cov.: 33

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.826 AC: 125766 AN: 152188 Hom.: 52878 Cov.: 33 AF XY: 0.818 AC XY: 60823 AN XY: 74392

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.824

Alfa AF: 0.840 Hom.: 50477

Bravo AF: 0.823

Asia WGS AF: 0.545 AC: 1894 AN: 3478

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

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16787; hg19: chr15-55800837;