rs2592991

Variant names:

• chr9-85385591-C-A
• rs2592991
• ENST00000648131.1:n.601-12631G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-85385591-C-A
• chr9-85385591-C-G
• chr9-85385591-C-T

Variant summary

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

The ENST00000648131.1(ENSG00000285634):​n.601-12631G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,242 control chromosomes in the GnomAD database, including 58,385 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 0.87 (58385 hom., cov: 31)
• Consequence: ENSG00000285634 ENST00000648131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 2 publications found

Genes affected

ENSG00000285634 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 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
ENSG00000285634	ENST00000648131.1	n.601-12631G>T		intron_variant	Intron 3 of 3
ENSG00000285634	ENST00000662737.1	n.1681-12631G>T		intron_variant	Intron 2 of 2
ENSG00000285634	ENST00000669133.1	n.283-12631G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132765 AN: 152124 Hom.: 58343 Cov.: 31

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.873 AC: 132863 AN: 152242 Hom.: 58385 Cov.: 31 AF XY: 0.873 AC XY: 64974 AN XY: 74450

African (AFR) AF: 0.948 AC: 39405 AN: 41556

American (AMR) AF: 0.730 AC: 11156 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4859 AN: 5180

South Asian (SAS) AF: 0.902 AC: 4350 AN: 4822

European-Finnish (FIN) AF: 0.889 AC: 9435 AN: 10608

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57852 AN: 68010

Other (OTH) AF: 0.873 AC: 1841 AN: 2110

Alfa AF: 0.859 Hom.: 81277

Bravo AF: 0.861

Asia WGS AF: 0.923 AC: 3212 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	1.4
DANN	Benign	0.40
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2592991; hg19: chr9-88000506;