15-78559273-G-A

Position:

• chr15-78559273-G-A

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 0.288 in 152,096 control chromosomes in the GnomAD database, including 6,845 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 0.29 (6845 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.346 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: 0.288 AC: 43709 AN: 151978 Hom.: 6838 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.288 AC: 43744 AN: 152096 Hom.: 6845 Cov.: 33 AF XY: 0.284 AC XY: 21105 AN XY: 74348

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.306

Alfa AF: 0.335 Hom.: 16215

Bravo AF: 0.277

Asia WGS AF: 0.134 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036527; hg19: chr15-78851615;