15-47918523-G-A

Variant names:

• chr15-47918523-G-A
• rs45552332
• ENST00000560900.1:n.195+34019G>A

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+34019G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 152,138 control chromosomes in the GnomAD database, including 75 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 0.010 (75 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 0 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+34019G>A		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.142+34019G>A		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.82+3161G>A		intron_variant	Intron 1 of 2
LOC124900354	XR_007064618.1	n.143-30833G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+34019G>A		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-74186G>A		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-74186G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0103 AC: 1570 AN: 152020 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.00294

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00510

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0104 AC: 1575 AN: 152138 Hom.: 75 Cov.: 32 AF XY: 0.0120 AC XY: 890 AN XY: 74374

African (AFR) AF: 0.00294 AC: 122 AN: 41556

American (AMR) AF: 0.0719 AC: 1099 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00511 AC: 26 AN: 5088

South Asian (SAS) AF: 0.0565 AC: 272 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000309 AC: 21 AN: 68008

Other (OTH) AF: 0.0166 AC: 35 AN: 2114

Alfa AF: 0.00770 Hom.: 3

Bravo AF: 0.0171

Asia WGS AF: 0.0370 AC: 129 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.63
PhyloP100		0.68
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs45552332; hg19: chr15-48210720;