11-116796764-C-T

Variant names:

• chr11-116796764-C-T
• rs633867

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.127 in 152,122 control chromosomes in the GnomAD database, including 2,377 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 0.13 (2377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 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: 0.127 AC: 19278 AN: 152004 Hom.: 2374 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.0555

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.127 AC: 19316 AN: 152122 Hom.: 2377 Cov.: 32 AF XY: 0.130 AC XY: 9689 AN XY: 74372

African (AFR) AF: 0.301 AC: 12481 AN: 41436

American (AMR) AF: 0.129 AC: 1970 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1770 AN: 5178

South Asian (SAS) AF: 0.0549 AC: 265 AN: 4826

European-Finnish (FIN) AF: 0.0898 AC: 951 AN: 10594

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.0214 AC: 1454 AN: 68018

Other (OTH) AF: 0.105 AC: 222 AN: 2110

Alfa AF: 0.0176 Hom.: 14

Bravo AF: 0.140

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.4
DANN	Benign	0.70
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs633867; hg19: chr11-116667480;