rs2589998

Variant names:

• chr7-138181624-C-T
• rs2589998
• ENST00000834913.1:n.283-7790C>T

Variant summary

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

The ENST00000834913.1(ENSG00000225559):​n.283-7790C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,068 control chromosomes in the GnomAD database, including 4,736 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 0.25 (4736 hom., cov: 31)
• Consequence: ENSG00000225559 ENST00000834913.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 2 publications found

Genes affected

ENSG00000225559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 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
ENSG00000225559	ENST00000834913.1	n.283-7790C>T		intron_variant	Intron 2 of 2
ENSG00000225559	ENST00000834914.1	n.263-1207C>T		intron_variant	Intron 2 of 3
ENSG00000225559	ENST00000834915.1	n.261-1207C>T		intron_variant	Intron 2 of 3
ENSG00000225559	ENST00000834916.1	n.397-1207C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37259 AN: 151950 Hom.: 4725 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0732

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.245 AC: 37297 AN: 152068 Hom.: 4736 Cov.: 31 AF XY: 0.244 AC XY: 18148 AN XY: 74338

African (AFR) AF: 0.212 AC: 8802 AN: 41458

American (AMR) AF: 0.187 AC: 2858 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3470

East Asian (EAS) AF: 0.0737 AC: 381 AN: 5168

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4820

European-Finnish (FIN) AF: 0.270 AC: 2852 AN: 10564

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18697 AN: 67996

Other (OTH) AF: 0.242 AC: 511 AN: 2108

Alfa AF: 0.267 Hom.: 4404

Bravo AF: 0.234

Asia WGS AF: 0.210 AC: 731 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	1.6
DANN	Benign	0.65
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs2589998; hg19: chr7-137866370;