15-48090740-G-A

Variant names:

• chr15-48090740-G-A
• rs733220
• ENST00000730753.1:n.64+9347G>A

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.64+9347G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

Genes affected

ENSG00000295542 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730753.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295542	ENST00000730753.1		n.64+9347G>A		intron	N/A

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

African (AFR) AF: 0.392 AC: 16239 AN: 41450

American (AMR) AF: 0.134 AC: 2041 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1897 AN: 5142

South Asian (SAS) AF: 0.0494 AC: 238 AN: 4822

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0360 AC: 2449 AN: 68000

Other (OTH) AF: 0.115 AC: 242 AN: 2112

Alfa AF: 0.110 Hom.: 790

Bravo AF: 0.178

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs733220; hg19: chr15-48382937;