15-48703189-G-T

Position:

• chr15-48703189-G-T

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 0.672 in 152,048 control chromosomes in the GnomAD database, including 36,032 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 0.67 (36032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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 (SAS) allele frequency at 95% confidence interval = 0.824 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: 0.672 AC: 102136 AN: 151928 Hom.: 36034 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.672 AC: 102162 AN: 152048 Hom.: 36032 Cov.: 31 AF XY: 0.681 AC XY: 50604 AN XY: 74344

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.694

Alfa AF: 0.735 Hom.: 69838

Bravo AF: 0.649

Asia WGS AF: 0.747 AC: 2593 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	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1072994; hg19: chr15-48995386;