rs7396851

Variant names:

• chr11-116813448-T-A
• rs7396851
• ENST00000457746.2:n.233A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-116813448-T-A
• chr11-116813448-T-C
• chr11-116813448-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000457746.2(LNC-RHL1):​n.233A>T variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LNC-RHL1 ENST00000457746.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.66
• Publications: 14 publications found

Genes affected

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

ENSG00000305923 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNC-RHL1	ENST00000457746.2	n.233A>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 2	5
LNC-RHL1	ENST00000814262.1	n.192A>T		non_coding_transcript_exon_variant	Exon 2 of 2
LNC-RHL1	ENST00000814263.1	n.158A>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.36
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7396851; hg19: chr11-116684164;