rs9582695

Variant names:

• chr13-103384086-A-G
• rs9582695
• ENST00000648788.1:n.56-8141A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-103384086-A-G
• chr13-103384086-A-T

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.56-8141A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,100 control chromosomes in the GnomAD database, including 1,502 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 0.13 (1502 hom., cov: 32)
• Consequence: ENSG00000285789 ENST00000648788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 1 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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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.56-8141A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20448 AN: 151982 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.134 AC: 20450 AN: 152100 Hom.: 1502 Cov.: 32 AF XY: 0.131 AC XY: 9722 AN XY: 74370

African (AFR) AF: 0.112 AC: 4632 AN: 41522

American (AMR) AF: 0.0912 AC: 1392 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3468

East Asian (EAS) AF: 0.0290 AC: 150 AN: 5180

South Asian (SAS) AF: 0.120 AC: 576 AN: 4814

European-Finnish (FIN) AF: 0.152 AC: 1609 AN: 10576

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11332 AN: 67956

Other (OTH) AF: 0.117 AC: 246 AN: 2110

Alfa AF: 0.143 Hom.: 881

Bravo AF: 0.128

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.36
DANN	Benign	0.82
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9582695; hg19: chr13-104036436;