11-116813312-T-C

Variant names:

• chr11-116813312-T-C
• rs7396835
• ENST00000457746.2:n.369A>G

Variant summary

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

The ENST00000814127.1(ENSG00000305923):​n.159T>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 0.84 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: ENSG00000305923 ENST00000814127.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 32 publications found

Genes affected

LNC-RHL1 (HGNC:56708): (lncRNA regulator of hepatic lineages 1)

ENSG00000305923 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814127.1. 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
	LNC-RHL1	ENST00000457746.2	TSL:5	n.369A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000305923	ENST00000814127.1		n.159T>C		non_coding_transcript_exon	Exon 1 of 2
	LNC-RHL1	ENST00000814262.1		n.328A>G		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.773 AC: 17 AN: 22

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.884 AC: 36658 AN: 41448

American (AMR) AF: 0.768 AC: 11688 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2806 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3499 AN: 5168

South Asian (SAS) AF: 0.652 AC: 3100 AN: 4756

European-Finnish (FIN) AF: 0.777 AC: 8215 AN: 10574

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.865 AC: 58744 AN: 67922

Other (OTH) AF: 0.827 AC: 1736 AN: 2100

Alfa AF: 0.834 Hom.: 15216

Bravo AF: 0.848

Asia WGS AF: 0.683 AC: 2379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-0.044

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7396835;

hg19: chr11-116684028;