15-48346598-G-T

Variant names:

• chr15-48346598-G-T
• rs4775748

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.798 in 152,124 control chromosomes in the GnomAD database, including 48,776 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 0.80 (48776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121391 AN: 152006 Hom.: 48755 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.798 AC: 121468 AN: 152124 Hom.: 48776 Cov.: 32 AF XY: 0.799 AC XY: 59452 AN XY: 74392

African (AFR) AF: 0.731 AC: 30310 AN: 41470

American (AMR) AF: 0.804 AC: 12289 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2841 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3056 AN: 5174

South Asian (SAS) AF: 0.786 AC: 3797 AN: 4830

European-Finnish (FIN) AF: 0.864 AC: 9144 AN: 10578

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57310 AN: 68006

Other (OTH) AF: 0.787 AC: 1659 AN: 2108

Alfa AF: 0.825 Hom.: 194056

Bravo AF: 0.792

Asia WGS AF: 0.676 AC: 2347 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.47
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4775748; hg19: chr15-48638795;