rs10520569

Variant names:

• chr15-84060637-C-T
• rs10520569
• ENST00000559921.1:n.54-6582G>A

Variant summary

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

The ENST00000741322.1(ENSG00000296726):​n.143+19408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 150,294 control chromosomes in the GnomAD database, including 911 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 0.098 (911 hom., cov: 32)
• Consequence: ENSG00000296726 ENST00000741322.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 5 publications found

Genes affected

ENSG00000259609 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741322.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259609	ENST00000559921.1	TSL:6	n.54-6582G>A		intron	N/A
	ENSG00000296726	ENST00000741322.1		n.143+19408G>A		intron	N/A
	ENSG00000296726	ENST00000741323.1		n.98-10859G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14643 AN: 150176 Hom.: 909 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0748

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0720

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0976 AC: 14662 AN: 150294 Hom.: 911 Cov.: 32 AF XY: 0.0969 AC XY: 7120 AN XY: 73448

African (AFR) AF: 0.0345 AC: 1423 AN: 41300

American (AMR) AF: 0.0747 AC: 1132 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.0887 AC: 303 AN: 3416

East Asian (EAS) AF: 0.163 AC: 840 AN: 5158

South Asian (SAS) AF: 0.0729 AC: 349 AN: 4790

European-Finnish (FIN) AF: 0.150 AC: 1539 AN: 10258

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8722 AN: 66926

Other (OTH) AF: 0.112 AC: 235 AN: 2098

Alfa AF: 0.119 Hom.: 609

Bravo AF: 0.0880

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10520569; hg19: chr15-84729389;