rs3884558

Variant names:

• chr15-61410580-A-G
• rs3884558
• ENST00000559783.2:n.187-10149T>C

Variant summary

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

The ENST00000559783.2(ENSG00000259675):​n.187-10149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,220 control chromosomes in the GnomAD database, including 54,504 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 0.84 (54504 hom., cov: 34)
• Consequence: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 15 publications found

Genes affected

ENSG00000259675 (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 (NFE) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370847	XR_932332.2	n.251-136A>G		intron_variant	Intron 1 of 2
LOC105370847	XR_932333.2	n.251-136A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259675	ENST00000559783.2	n.187-10149T>C		intron_variant	Intron 3 of 4	3
ENSG00000310047	ENST00000846750.1	n.270-136A>G		intron_variant	Intron 1 of 1
ENSG00000310047	ENST00000846751.1	n.267-136A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127381 AN: 152102 Hom.: 54468 Cov.: 34

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.837 AC: 127461 AN: 152220 Hom.: 54504 Cov.: 34 AF XY: 0.827 AC XY: 61569 AN XY: 74406

African (AFR) AF: 0.826 AC: 34283 AN: 41528

American (AMR) AF: 0.668 AC: 10218 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3017 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1965 AN: 5180

South Asian (SAS) AF: 0.781 AC: 3761 AN: 4818

European-Finnish (FIN) AF: 0.862 AC: 9131 AN: 10588

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.915 AC: 62233 AN: 68028

Other (OTH) AF: 0.831 AC: 1751 AN: 2106

Alfa AF: 0.881 Hom.: 191149

Bravo AF: 0.816

Asia WGS AF: 0.582 AC: 2027 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	0.20
DANN	Benign	0.73
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs3884558; hg19: chr15-61702779;