11-116813448-T-C

Variant names:

• chr11-116813448-T-C
• rs7396851
• ENST00000457746.1:n.89A>G

Variant summary

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

The ENST00000457746.1(ENSG00000236267):​n.89A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 151,898 control chromosomes in the GnomAD database, including 51,493 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 0.82 (51487 hom., cov: 31)
  • Exomes 𝑓: 1.0 (6 hom.)
• Consequence: ENSG00000236267 ENST00000457746.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66

Genes affected

ENSG00000236267 (HGNC:56708): (lncRNA regulator of hepatic lineages 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNC-RHL1	XR_007062898.1	n.273A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236267	ENST00000457746.1	n.89A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124503 AN: 151768 Hom.: 51476 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.816

GnomAD4 exome AF: 1.00 AC: 12 AN: 12 Hom.: 6 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.820 AC: 124564 AN: 151886 Hom.: 51487 Cov.: 31 AF XY: 0.810 AC XY: 60132 AN XY: 74232

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.812

Alfa AF: 0.834 Hom.: 8409

Bravo AF: 0.826

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7396851; hg19: chr11-116684164;