chr11-118870448-T-C

Variant names:

• chr11-118870448-T-C
• rs7117261

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 0.8 in 152,110 control chromosomes in the GnomAD database, including 48,669 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 0.80 (48669 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.800 AC: 121565 AN: 151992 Hom.: 48642 Cov.: 31

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.800 AC: 121645 AN: 152110 Hom.: 48669 Cov.: 31 AF XY: 0.803 AC XY: 59670 AN XY: 74344

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.845

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.822

Alfa AF: 0.799 Hom.: 6039

Bravo AF: 0.800

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7117261; hg19: chr11-118741157;