15-47954757-A-G

Variant names:

• chr15-47954757-A-G
• rs751467
• ENST00000560900.1:n.196-37952A>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.196-37952A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,038 control chromosomes in the GnomAD database, including 34,946 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 0.67 (34946 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-37952A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-37952A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-37952A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-37952A>G		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-37952A>G		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-37952A>G		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.69-37952A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102016 AN: 151920 Hom.: 34891 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.672 AC: 102138 AN: 152038 Hom.: 34946 Cov.: 32 AF XY: 0.672 AC XY: 49930 AN XY: 74308

African (AFR) AF: 0.789 AC: 32739 AN: 41486

American (AMR) AF: 0.648 AC: 9909 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2028 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4420 AN: 5160

South Asian (SAS) AF: 0.668 AC: 3220 AN: 4818

European-Finnish (FIN) AF: 0.647 AC: 6836 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.603 AC: 40964 AN: 67932

Other (OTH) AF: 0.645 AC: 1364 AN: 2116

Alfa AF: 0.623 Hom.: 23380

Bravo AF: 0.677

Asia WGS AF: 0.774 AC: 2695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.65
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs751467; hg19: chr15-48246954;