rs2869046

Positions:

• chr15-78428624-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;