rs7589525

Variant names:

• chr2-102029929-A-C
• rs7589525

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 0.242 in 152,126 control chromosomes in the GnomAD database, including 4,923 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 0.24 (4923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.276 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: 0.242 AC: 36792 AN: 152008 Hom.: 4914 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.242 AC: 36827 AN: 152126 Hom.: 4923 Cov.: 32 AF XY: 0.247 AC XY: 18376 AN XY: 74368

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.243

Alfa AF: 0.254 Hom.: 10262

Bravo AF: 0.233

Asia WGS AF: 0.194 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7589525; hg19: chr2-102646391; COSMIC: COSV60206438;