10-52729095-A-G

Variant names:

• chr10-52729095-A-G
• rs10824779
• ENST00000443523.3:n.123+26215T>C

Variant summary

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

The ENST00000443523.3(LNCAROD):​n.123+26215T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,036 control chromosomes in the GnomAD database, including 19,459 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 0.48 (19459 hom., cov: 33)
• Consequence: LNCAROD ENST00000443523.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 5 publications found

Genes affected

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

LOC105378305 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443523.3. 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
	LOC105378305	NR_155748.1		n.95+26215T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCAROD	ENST00000443523.3	TSL:2	n.123+26215T>C		intron	N/A
	LNCAROD	ENST00000448017.3	TSL:2	n.221+26211T>C		intron	N/A
	LNCAROD	ENST00000647908.1		n.100-5077T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72898 AN: 151918 Hom.: 19453 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.480 AC: 72924 AN: 152036 Hom.: 19459 Cov.: 33 AF XY: 0.482 AC XY: 35798 AN XY: 74332

African (AFR) AF: 0.229 AC: 9482 AN: 41494

American (AMR) AF: 0.611 AC: 9333 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1961 AN: 3472

East Asian (EAS) AF: 0.577 AC: 2984 AN: 5168

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4820

European-Finnish (FIN) AF: 0.494 AC: 5214 AN: 10558

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39518 AN: 67948

Other (OTH) AF: 0.500 AC: 1054 AN: 2108

Alfa AF: 0.541 Hom.: 3987

Bravo AF: 0.480

Asia WGS AF: 0.567 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.63
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10824779; hg19: chr10-54488855;