rs2869046

Variant names:

• chr15-78428624-T-C
• rs2869046

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.415

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2869046; hg19: chr15-78720966;