rs1480090

Variant names:

• chr15-98172432-C-A
• rs1480090
• ENST00000560360.2:n.313+85147G>T

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.313+85147G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,802 control chromosomes in the GnomAD database, including 22,028 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 0.54 (22028 hom., cov: 30)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 6 publications found

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259199	ENST00000560360.2	n.313+85147G>T		intron_variant	Intron 3 of 4	5
ENSG00000259199	ENST00000717124.1	n.291+85147G>T		intron_variant	Intron 3 of 8
ENSG00000305856	ENST00000813524.1	n.71+5667G>T		intron_variant	Intron 1 of 4
ENSG00000305856	ENST00000813525.1	n.145+5667G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81411 AN: 151684 Hom.: 22009 Cov.: 30

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.537 AC: 81475 AN: 151802 Hom.: 22028 Cov.: 30 AF XY: 0.536 AC XY: 39800 AN XY: 74192

African (AFR) AF: 0.577 AC: 23863 AN: 41372

American (AMR) AF: 0.591 AC: 9010 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1558 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3571 AN: 5170

South Asian (SAS) AF: 0.551 AC: 2651 AN: 4808

European-Finnish (FIN) AF: 0.472 AC: 4954 AN: 10506

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.502 AC: 34120 AN: 67914

Other (OTH) AF: 0.528 AC: 1113 AN: 2106

Alfa AF: 0.516 Hom.: 34642

Bravo AF: 0.549

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.82
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1480090; hg19: chr15-98715661;