rs11155053

Variant names:

• chr6-139338875-C-T
• rs11155053
• ENST00000403909.2:n.768C>T

Variant summary

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

The ENST00000775951.1(ENSG00000301069):​n.772C>T 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 0.104 in 545,186 control chromosomes in the GnomAD database, including 3,563 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 0.11 (1092 hom., cov: 33)
  • Exomes 𝑓: 0.10 (2471 hom.)
• Consequence: ENSG00000301069 ENST00000775951.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66
• Publications: 6 publications found

Genes affected

ENSG00000218565 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775951.1. 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
	ENSG00000218565	ENST00000403909.2	TSL:6	n.768C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000301069	ENST00000775951.1		n.772C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000226571	ENST00000650173.1		n.509+51973C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16898 AN: 152064 Hom.: 1092 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0530

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.101 AC: 39770 AN: 393004 Hom.: 2471 Cov.: 4 AF XY: 0.0989 AC XY: 20846 AN XY: 210696

African (AFR) AF: 0.127 AC: 1395 AN: 10942

American (AMR) AF: 0.0569 AC: 946 AN: 16630

Ashkenazi Jewish (ASJ) AF: 0.0724 AC: 794 AN: 10972

East Asian (EAS) AF: 0.00153 AC: 40 AN: 26122

South Asian (SAS) AF: 0.0596 AC: 2504 AN: 42028

European-Finnish (FIN) AF: 0.175 AC: 4588 AN: 26164

Middle Eastern (MID) AF: 0.102 AC: 168 AN: 1652

European-Non Finnish (NFE) AF: 0.115 AC: 27098 AN: 236388

Other (OTH) AF: 0.101 AC: 2237 AN: 22106

GnomAD4 genome AF: 0.111 AC: 16893 AN: 152182 Hom.: 1092 Cov.: 33 AF XY: 0.111 AC XY: 8271 AN XY: 74408

African (AFR) AF: 0.126 AC: 5232 AN: 41500

American (AMR) AF: 0.0784 AC: 1198 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.0526 AC: 254 AN: 4830

European-Finnish (FIN) AF: 0.187 AC: 1973 AN: 10572

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7660 AN: 68014

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.106 Hom.: 1949

Bravo AF: 0.105

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs11155053; hg19: chr6-139660012;