chr15-89567719-C-T

Variant names:

• chr15-89567719-C-T
• rs11639117
• ENST00000559041.1:n.48-23784C>T

Variant summary

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

The ENST00000559041.1(ENSG00000259713):​n.48-23784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 146,524 control chromosomes in the GnomAD database, including 22,310 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 0.55 (22310 hom., cov: 24)
• Consequence: ENSG00000259713 ENST00000559041.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486
• Publications: 4 publications found

Genes affected

ENSG00000259713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559041.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259713	ENST00000559041.1	TSL:5	n.48-23784C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 80654 AN: 146416 Hom.: 22301 Cov.: 24

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.551 AC: 80700 AN: 146524 Hom.: 22310 Cov.: 24 AF XY: 0.548 AC XY: 38982 AN XY: 71124

African (AFR) AF: 0.476 AC: 18967 AN: 39816

American (AMR) AF: 0.495 AC: 7204 AN: 14540

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1921 AN: 3422

East Asian (EAS) AF: 0.310 AC: 1535 AN: 4946

South Asian (SAS) AF: 0.500 AC: 2240 AN: 4478

European-Finnish (FIN) AF: 0.625 AC: 5984 AN: 9582

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.616 AC: 41009 AN: 66532

Other (OTH) AF: 0.547 AC: 1104 AN: 2020

Alfa AF: 0.574 Hom.: 30992

Bravo AF: 0.526

Asia WGS AF: 0.400 AC: 1393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.2
DANN	Benign	0.37
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs11639117; hg19: chr15-90110950;