chr15-85802824-G-A

Position:

• chr15-85802824-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 0.355 in 151,968 control chromosomes in the GnomAD database, including 10,432 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 0.36 (10432 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.355 AC: 53946 AN: 151850 Hom.: 10419 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.355 AC: 53994 AN: 151968 Hom.: 10432 Cov.: 33 AF XY: 0.348 AC XY: 25853 AN XY: 74310

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.325

Alfa AF: 0.315 Hom.: 15636

Bravo AF: 0.370

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9635398; hg19: chr15-86346055;