rs7117196

Variant names:

• chr11-103533183-C-T
• rs7117196

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 0.472 in 152,022 control chromosomes in the GnomAD database, including 19,382 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 0.47 (19382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

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 (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.472 AC: 71732 AN: 151904 Hom.: 19378 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.472 AC: 71755 AN: 152022 Hom.: 19382 Cov.: 32 AF XY: 0.467 AC XY: 34690 AN XY: 74314

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.509

Alfa AF: 0.591 Hom.: 27681

Bravo AF: 0.452

Asia WGS AF: 0.335 AC: 1165 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	3.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7117196; hg19: chr11-103403911; COSMIC: COSV53887172;