chr15-48077906-G-T

Position:

• chr15-48077906-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 0.0836 in 152,184 control chromosomes in the GnomAD database, including 689 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 0.084 (689 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48077906G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0834 AC: 12682 AN: 152068 Hom.: 682 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0466

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0836 AC: 12718 AN: 152184 Hom.: 689 Cov.: 32 AF XY: 0.0840 AC XY: 6246 AN XY: 74398

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0680

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0930

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0466

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0640 Hom.: 118

Bravo AF: 0.0943

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	2.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960541; hg19: chr15-48370103;