15-45207849-A-G

Position:

• chr15-45207849-A-G

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 0.152 in 150,500 control chromosomes in the GnomAD database, including 2,180 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 0.15 (2180 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.152 AC: 22922 AN: 150388 Hom.: 2180 Cov.: 29

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.0861

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.152 AC: 22927 AN: 150500 Hom.: 2180 Cov.: 29 AF XY: 0.153 AC XY: 11236 AN XY: 73378

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.162

Alfa AF: 0.173 Hom.: 905

Bravo AF: 0.149

Asia WGS AF: 0.218 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765787; hg19: chr15-45500047;