11-116567039-C-T

Variant names:

• chr11-116567039-C-T
• rs11605293

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 0.21 in 151,198 control chromosomes in the GnomAD database, including 6,203 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 0.21 (6203 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.210 AC: 31719 AN: 151080 Hom.: 6189 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0858

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.210 AC: 31777 AN: 151198 Hom.: 6203 Cov.: 31 AF XY: 0.203 AC XY: 15001 AN XY: 73854

African (AFR) AF: 0.523 AC: 21473 AN: 41050

American (AMR) AF: 0.113 AC: 1725 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0858 AC: 297 AN: 3462

East Asian (EAS) AF: 0.0770 AC: 394 AN: 5116

South Asian (SAS) AF: 0.100 AC: 480 AN: 4782

European-Finnish (FIN) AF: 0.0545 AC: 569 AN: 10432

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0925 AC: 6278 AN: 67836

Other (OTH) AF: 0.187 AC: 393 AN: 2100

Alfa AF: 0.121 Hom.: 3121

Bravo AF: 0.229

Asia WGS AF: 0.110 AC: 381 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	3.6
DANN	Benign	0.57
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs11605293; hg19: chr11-116437756;