rs9587939

Variant names:

• chr13-109632604-C-A
• rs9587939
• ENST00000650264.1:n.759-61446G>T

Your query was ambiguous. Multiple possible variants found:

• chr13-109632604-C-A
• chr13-109632604-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650264.1(ENSG00000285534):​n.759-61446G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,006 control chromosomes in the GnomAD database, including 2,735 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 0.19 (2735 hom., cov: 31)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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
ENSG00000285534	ENST00000650264.1	n.759-61446G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28180 AN: 151888 Hom.: 2728 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.186 AC: 28217 AN: 152006 Hom.: 2735 Cov.: 31 AF XY: 0.185 AC XY: 13771 AN XY: 74288

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.186

Alfa AF: 0.151 Hom.: 1004

Bravo AF: 0.181

Asia WGS AF: 0.271 AC: 942 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	0.40
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9587939; hg19: chr13-110284951;