chr10-52541980-A-T

Variant names:

• chr10-52541980-A-T
• rs7085224
• ENST00000647908.1:n.385+14545T>A

Variant summary

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

The ENST00000647908.1(LNCAROD):​n.385+14545T>A variant causes a intron 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: 30)
• Consequence: LNCAROD ENST00000647908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 3 publications found

Genes affected

LNCAROD (HGNC:50913): (lncRNA activating regulator of DKK1)

ENSG00000296101 (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=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902426	XR_007062146.1	n.67+8591A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCAROD	ENST00000647908.1	n.385+14545T>A		intron_variant	Intron 4 of 6
LNCAROD	ENST00000736176.1	n.322-8596T>A		intron_variant	Intron 4 of 4
LNCAROD	ENST00000736177.1	n.384-8596T>A		intron_variant	Intron 4 of 4
ENSG00000296101	ENST00000736443.1	n.274-37710A>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 30

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.72
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs7085224; hg19: chr10-54301740;