15-48108002-A-G

Variant names:

• chr15-48108002-A-G
• rs2675345
• ENST00000730753.1:n.65-613A>G

Variant summary

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

The ENST00000730753.1(ENSG00000295542):​n.65-613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,158 control chromosomes in the GnomAD database, including 15,691 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 0.28 (15691 hom., cov: 32)
• Consequence: ENSG00000295542 ENST00000730753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 24 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903485	XR_007064619.1	n.183-1105T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295542	ENST00000730753.1	n.65-613A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42646 AN: 152040 Hom.: 15616 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.00424

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.00407

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.281 AC: 42791 AN: 152158 Hom.: 15691 Cov.: 32 AF XY: 0.281 AC XY: 20880 AN XY: 74420

African (AFR) AF: 0.797 AC: 33042 AN: 41458

American (AMR) AF: 0.267 AC: 4087 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3795 AN: 5164

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4826

European-Finnish (FIN) AF: 0.00424 AC: 45 AN: 10620

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00407 AC: 277 AN: 68006

Other (OTH) AF: 0.224 AC: 473 AN: 2116

Alfa AF: 0.383 Hom.: 8606

Bravo AF: 0.328

Asia WGS AF: 0.567 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.49
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2675345; hg19: chr15-48400199;