rs7130929

Variant names:

• chr11-18046616-C-A
• rs7130929

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 0.4 in 151,902 control chromosomes in the GnomAD database, including 12,396 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 0.40 (12396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.400 AC: 60706 AN: 151784 Hom.: 12386 Cov.: 31

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.400 AC: 60762 AN: 151902 Hom.: 12396 Cov.: 31 AF XY: 0.394 AC XY: 29249 AN XY: 74226

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.415

Alfa AF: 0.410 Hom.: 17210

Bravo AF: 0.399

Asia WGS AF: 0.301 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7130929; hg19: chr11-18068163;