15-48090740-G-A

Position:

• chr15-48090740-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 0.155 in 152,070 control chromosomes in the GnomAD database, including 3,795 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 (3795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 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: 0.154 AC: 23449 AN: 151952 Hom.: 3785 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.155 AC: 23516 AN: 152070 Hom.: 3795 Cov.: 32 AF XY: 0.152 AC XY: 11299 AN XY: 74340

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.0494

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0869 Hom.: 288

Bravo AF: 0.178

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733220; hg19: chr15-48382937;