rs11155053

Positions:

• chr6-139338875-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000403909.2(ENSG00000218565):​n.768C>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: ENSG00000218565 ENST00000403909.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.66

Genes affected

ENSG00000218565 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100129844		n.139338875C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000218565	ENST00000403909.2	n.768C>T		non_coding_transcript_exon_variant	2/2	6
ENSG00000226571	ENST00000650173.1	n.509+51973C>T		intron_variant

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

Gnomad4 AFR exome AF: 0.127

Gnomad4 AMR exome AF: 0.0569

Gnomad4 ASJ exome AF: 0.0724

Gnomad4 EAS exome AF: 0.00153

Gnomad4 SAS exome AF: 0.0596

Gnomad4 FIN exome AF: 0.175

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.101

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

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0784

Gnomad4 ASJ AF: 0.0662

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0526

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.101

Alfa AF: 0.105 Hom.: 1233

Bravo AF: 0.105

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11155053; hg19: chr6-139660012;