rs2598592

Variant names:

• chr2-2586609-C-T
• rs2598592
• ENST00000806417.1:n.248-10295G>A

Variant summary

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

The ENST00000806417.1(ENSG00000290112):​n.248-10295G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 151,946 control chromosomes in the GnomAD database, including 27,285 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 0.59 (27285 hom., cov: 32)
• Consequence: ENSG00000290112 ENST00000806417.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 6 publications found

Genes affected

ENSG00000290112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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
ENSG00000290112	ENST00000806417.1	n.248-10295G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89385 AN: 151828 Hom.: 27278 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.589 AC: 89423 AN: 151946 Hom.: 27285 Cov.: 32 AF XY: 0.600 AC XY: 44553 AN XY: 74244

African (AFR) AF: 0.471 AC: 19534 AN: 41440

American (AMR) AF: 0.739 AC: 11294 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2041 AN: 3468

East Asian (EAS) AF: 0.976 AC: 5026 AN: 5152

South Asian (SAS) AF: 0.786 AC: 3789 AN: 4822

European-Finnish (FIN) AF: 0.619 AC: 6511 AN: 10518

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39200 AN: 67950

Other (OTH) AF: 0.604 AC: 1275 AN: 2112

Alfa AF: 0.585 Hom.: 96379

Bravo AF: 0.593

Asia WGS AF: 0.838 AC: 2910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.45
DANN	Benign	0.69
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2598592; hg19: chr2-2590381;