chr15-78428624-T-C

Variant names:

• chr15-78428624-T-C
• rs2869046

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.399 in 151,046 control chromosomes in the GnomAD database, including 13,063 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (13063 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 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: 0.400 AC: 60315 AN: 150928 Hom.: 13059 Cov.: 28

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.399 AC: 60334 AN: 151046 Hom.: 13063 Cov.: 28 AF XY: 0.403 AC XY: 29670 AN XY: 73702

African (AFR) AF: 0.230 AC: 9451 AN: 41034

American (AMR) AF: 0.360 AC: 5470 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1514 AN: 3462

East Asian (EAS) AF: 0.483 AC: 2476 AN: 5124

South Asian (SAS) AF: 0.510 AC: 2434 AN: 4770

European-Finnish (FIN) AF: 0.460 AC: 4780 AN: 10386

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32807 AN: 67778

Other (OTH) AF: 0.415 AC: 868 AN: 2094

Alfa AF: 0.434 Hom.: 1885

Bravo AF: 0.385

Asia WGS AF: 0.441 AC: 1532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.54
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2869046; hg19: chr15-78720966;