11-118870448-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;