rs11155133

Variant names:

• chr6-140848688-A-G
• rs11155133
• ENST00000683183.1:n.584T>C

Variant summary

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

The ENST00000683183.1(ENSG00000234147):​n.584T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 151,948 control chromosomes in the GnomAD database, including 1,213 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 0.083 (1213 hom., cov: 32)
• Consequence: ENSG00000234147 ENST00000683183.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 17 publications found

Genes affected

ENSG00000234147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000683183.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234147	ENST00000683183.1		n.584T>C		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000234147	ENST00000455011.3	TSL:5	n.264-2384T>C		intron	N/A
	ENSG00000234147	ENST00000650553.2		n.195-32458T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12642 AN: 151830 Hom.: 1207 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00800

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0835 AC: 12681 AN: 151948 Hom.: 1213 Cov.: 32 AF XY: 0.0847 AC XY: 6295 AN XY: 74306

African (AFR) AF: 0.226 AC: 9337 AN: 41360

American (AMR) AF: 0.0909 AC: 1386 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3470

East Asian (EAS) AF: 0.117 AC: 603 AN: 5174

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4822

European-Finnish (FIN) AF: 0.0118 AC: 125 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00799 AC: 543 AN: 67956

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.0426 Hom.: 1112

Bravo AF: 0.0977

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11155133; hg19: chr6-141169825;