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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723724	XR_428030.5	n.344-2384T>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234147	ENST00000683183.1	n.584T>C		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000234147	ENST00000455011.3	n.264-2384T>C		intron_variant	Intron 3 of 3	5
ENSG00000234147	ENST00000650553.2	n.195-32458T>C		intron_variant	Intron 1 of 4

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 v4.3

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;