rs9582694

Variant names:

• chr13-103373924-A-C
• rs9582694
• ENST00000648788.1:n.56-18303A>C

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.56-18303A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,952 control chromosomes in the GnomAD database, including 2,272 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 0.16 (2272 hom., cov: 32)
• Consequence: ENSG00000285789 ENST00000648788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 2 publications found

Genes affected

ENSG00000285789 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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
ENSG00000285789	ENST00000648788.1	n.56-18303A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24988 AN: 151834 Hom.: 2269 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.165 AC: 25017 AN: 151952 Hom.: 2272 Cov.: 32 AF XY: 0.161 AC XY: 11960 AN XY: 74244

African (AFR) AF: 0.225 AC: 9321 AN: 41470

American (AMR) AF: 0.0977 AC: 1489 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3468

East Asian (EAS) AF: 0.0548 AC: 282 AN: 5150

South Asian (SAS) AF: 0.130 AC: 628 AN: 4822

European-Finnish (FIN) AF: 0.152 AC: 1612 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10908 AN: 67910

Other (OTH) AF: 0.140 AC: 295 AN: 2104

Alfa AF: 0.159 Hom.: 8915

Bravo AF: 0.162

Asia WGS AF: 0.0940 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.75
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9582694; hg19: chr13-104026274;