rs2589998

Variant names:

• chr7-138181624-C-T
• rs2589998

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0737

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.242

Alfa AF: 0.267 Hom.: 3745

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2589998; hg19: chr7-137866370;