11-116813312-T-C

Position:

• chr11-116813312-T-C

Variant summary

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

The ENST00000457746.1(ENSG00000236267):​n.225A>G 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 0.84 in 151,896 control chromosomes in the GnomAD database, including 54,017 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 0.84 (54007 hom., cov: 30)
  • Exomes 𝑓: 0.75 (10 hom.)
• Consequence: ENSG00000236267 ENST00000457746.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

Genes affected

ENSG00000236267 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LNC-RHL1	XR_007062898.1	n.409A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000236267	ENST00000457746.1	n.225A>G		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127457 AN: 151746 Hom.: 53976 Cov.: 30

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.831

GnomAD4 exome AF: 0.750 AC: 24 AN: 32 Hom.: 10 Cov.: 0 AF XY: 0.808 AC XY: 21 AN XY: 26

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.750

Gnomad4 NFE exome AF: 0.773

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.840 AC: 127543 AN: 151864 Hom.: 54007 Cov.: 30 AF XY: 0.829 AC XY: 61542 AN XY: 74196

Gnomad4 AFR AF: 0.884

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.827

Alfa AF: 0.838 Hom.: 6474

Bravo AF: 0.848

Asia WGS AF: 0.683 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7396835; hg19: chr11-116684028;