rs16787

Variant names:

• chr15-55508639-G-T
• rs16787

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.879 AC: 36522 AN: 41526

American (AMR) AF: 0.780 AC: 11914 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2777 AN: 3470

East Asian (EAS) AF: 0.323 AC: 1667 AN: 5166

South Asian (SAS) AF: 0.641 AC: 3093 AN: 4824

European-Finnish (FIN) AF: 0.825 AC: 8745 AN: 10594

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.856 AC: 58238 AN: 68024

Other (OTH) AF: 0.824 AC: 1736 AN: 2106

Alfa AF: 0.834 Hom.: 74804

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

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-1.3
PromoterAI		0.0072	Neutral

Splicing

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

Other links and lift over

dbSNP: rs16787; hg19: chr15-55800837;