15-78384471-G-C

Position:

• chr15-78384471-G-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 0.839 in 152,184 control chromosomes in the GnomAD database, including 53,818 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 0.84 (53818 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127627 AN: 152066 Hom.: 53758 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.839 AC: 127748 AN: 152184 Hom.: 53818 Cov.: 32 AF XY: 0.841 AC XY: 62547 AN XY: 74372

Gnomad4 AFR AF: 0.922

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.854

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.831

Alfa AF: 0.771 Hom.: 2199

Bravo AF: 0.854

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4243079; hg19: chr15-78676813;