chr15-78396492-C-T

Variant names:

• chr15-78396492-C-T
• rs2869040

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 0.658 in 152,026 control chromosomes in the GnomAD database, including 33,564 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 0.66 (33564 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.793 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: 0.658 AC: 99928 AN: 151908 Hom.: 33519 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.658 AC: 100031 AN: 152026 Hom.: 33564 Cov.: 31 AF XY: 0.660 AC XY: 49062 AN XY: 74286

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.654

Alfa AF: 0.591 Hom.: 37856

Bravo AF: 0.664

Asia WGS AF: 0.700 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2869040; hg19: chr15-78688834;