rs7130588

Variant names:

• chr11-76559639-A-G
• rs7130588

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 0.285 in 152,036 control chromosomes in the GnomAD database, including 6,600 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 0.29 (6600 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 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: 0.285 AC: 43341 AN: 151918 Hom.: 6601 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.285 AC: 43355 AN: 152036 Hom.: 6600 Cov.: 31 AF XY: 0.279 AC XY: 20768 AN XY: 74324

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.0927

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.310

Alfa AF: 0.340 Hom.: 20246

Bravo AF: 0.283

Asia WGS AF: 0.165 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7130588; hg19: chr11-76270683;