rs952124

Variant names:

• chr3-153691006-C-T
• rs952124
• ENST00000493214.2:n.78-18749G>A

Variant summary

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

The ENST00000493214.2(LINC02006):​n.78-18749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,918 control chromosomes in the GnomAD database, including 23,553 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 0.53 (23553 hom., cov: 32)
• Consequence: LINC02006 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 4 publications found

Genes affected

LINC02006 (HGNC:52842): (long intergenic non-protein coding RNA 2006)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493214.2. 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
	LINC02006	NR_146713.1		n.78-18749G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02006	ENST00000493214.2	TSL:2	n.78-18749G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80488 AN: 151800 Hom.: 23550 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.0803

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.530 AC: 80512 AN: 151918 Hom.: 23553 Cov.: 32 AF XY: 0.523 AC XY: 38856 AN XY: 74272

African (AFR) AF: 0.354 AC: 14662 AN: 41450

American (AMR) AF: 0.467 AC: 7109 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1859 AN: 3472

East Asian (EAS) AF: 0.0801 AC: 414 AN: 5166

South Asian (SAS) AF: 0.328 AC: 1579 AN: 4810

European-Finnish (FIN) AF: 0.722 AC: 7636 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.669 AC: 45420 AN: 67908

Other (OTH) AF: 0.509 AC: 1076 AN: 2112

Alfa AF: 0.603 Hom.: 15739

Bravo AF: 0.501

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.77
PhyloP100		-0.35

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: rs952124;

hg19: chr3-153408795;