11-116728676-C-T

Variant names:

• chr11-116728676-C-T
• rs180358

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 0.19 in 152,186 control chromosomes in the GnomAD database, including 2,965 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 0.19 (2965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.603
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 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: 0.190 AC: 28828 AN: 152068 Hom.: 2962 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.190 AC: 28853 AN: 152186 Hom.: 2965 Cov.: 32 AF XY: 0.186 AC XY: 13877 AN XY: 74408

African (AFR) AF: 0.174 AC: 7229 AN: 41522

American (AMR) AF: 0.143 AC: 2187 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3470

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5184

South Asian (SAS) AF: 0.104 AC: 503 AN: 4824

European-Finnish (FIN) AF: 0.227 AC: 2404 AN: 10588

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15053 AN: 67988

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.205 Hom.: 10560

Bravo AF: 0.184

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.1
DANN	Benign	0.47
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs180358; hg19: chr11-116599392;