rs9530579

Variant names:

• chr13-76651467-A-G
• rs9530579
• ENST00000648060.1:n.395+77878T>C

Variant summary

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

The ENST00000648060.1(ENSG00000285572):​n.395+77878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,192 control chromosomes in the GnomAD database, including 4,901 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 0.22 (4901 hom., cov: 32)
• Consequence: ENSG00000285572 ENST00000648060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695
• Publications: 3 publications found

Genes affected

ENSG00000285572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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
ENSG00000285572	ENST00000648060.1	n.395+77878T>C		intron_variant	Intron 3 of 4
ENSG00000285572	ENST00000791171.1	n.142+37755T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33920 AN: 152074 Hom.: 4900 Cov.: 32

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.223 AC: 33914 AN: 152192 Hom.: 4901 Cov.: 32 AF XY: 0.222 AC XY: 16555 AN XY: 74406

African (AFR) AF: 0.0560 AC: 2326 AN: 41562

American (AMR) AF: 0.289 AC: 4416 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5184

South Asian (SAS) AF: 0.266 AC: 1285 AN: 4822

European-Finnish (FIN) AF: 0.274 AC: 2899 AN: 10594

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21045 AN: 67972

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.278 Hom.: 4689

Bravo AF: 0.215

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.88
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs9530579; hg19: chr13-77225602;