rs2869036

Variant names:

• chr15-78375230-G-A
• rs2869036

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 0.811 in 152,042 control chromosomes in the GnomAD database, including 50,343 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 0.81 (50343 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28

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 (AFR) allele frequency at 95% confidence interval = 0.907 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: 0.811 AC: 123179 AN: 151924 Hom.: 50275 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.811 AC: 123308 AN: 152042 Hom.: 50343 Cov.: 30 AF XY: 0.812 AC XY: 60323 AN XY: 74296

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.804

Alfa AF: 0.769 Hom.: 15565

Bravo AF: 0.817

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.052
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2869036; hg19: chr15-78667572;