rs7588926

Variant names:

• chr2-27120026-C-T
• rs7588926

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 0.124 in 152,034 control chromosomes in the GnomAD database, including 1,547 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 0.12 (1547 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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 (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.124 AC: 18863 AN: 151916 Hom.: 1546 Cov.: 31

Gnomad AFR AF: 0.0330

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.124 AC: 18867 AN: 152034 Hom.: 1547 Cov.: 31 AF XY: 0.124 AC XY: 9223 AN XY: 74298

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.123

Alfa AF: 0.148 Hom.: 301

Bravo AF: 0.109

Asia WGS AF: 0.0410 AC: 144 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	0.89
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: rs7588926; hg19: chr2-27342894;