rs7118530

Variant names:

• chr11-114019403-T-C
• rs7118530

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 0.313 in 152,102 control chromosomes in the GnomAD database, including 7,782 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 0.31 (7782 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 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: 0.313 AC: 47557 AN: 151984 Hom.: 7781 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.313 AC: 47571 AN: 152102 Hom.: 7782 Cov.: 33 AF XY: 0.311 AC XY: 23152 AN XY: 74360

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.340

Alfa AF: 0.352 Hom.: 19430

Bravo AF: 0.309

Asia WGS AF: 0.290 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7118530; hg19: chr11-113890125;