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. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650264.1. 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
	ENSG00000285534	ENST00000650264.1		n.759-61446G>T		intron	N/A

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

African (AFR) AF: 0.236 AC: 9767 AN: 41452

American (AMR) AF: 0.113 AC: 1723 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3464

East Asian (EAS) AF: 0.297 AC: 1527 AN: 5150

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4824

European-Finnish (FIN) AF: 0.188 AC: 1986 AN: 10550

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10825 AN: 67982

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.153 Hom.: 1134

Bravo AF: 0.181

Asia WGS AF: 0.271 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.41
PhyloP100		-2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9587939;

hg19: chr13-110284951;