3-153690873-T-C

Variant names:

• chr3-153690873-T-C
• rs952122
• ENST00000493214.2:n.78-18616A>G

Variant summary

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

The ENST00000493214.2(LINC02006):​n.78-18616A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,808 control chromosomes in the GnomAD database, including 24,666 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 0.55 (24666 hom., cov: 31)
• Consequence: LINC02006 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.645 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.78-18616A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02006	ENST00000493214.2	TSL:2	n.78-18616A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83847 AN: 151690 Hom.: 24660 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.553 AC: 83883 AN: 151808 Hom.: 24666 Cov.: 31 AF XY: 0.545 AC XY: 40428 AN XY: 74192

African (AFR) AF: 0.462 AC: 19125 AN: 41358

American (AMR) AF: 0.472 AC: 7189 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3468

East Asian (EAS) AF: 0.0886 AC: 457 AN: 5156

South Asian (SAS) AF: 0.328 AC: 1580 AN: 4816

European-Finnish (FIN) AF: 0.720 AC: 7581 AN: 10534

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44191 AN: 67926

Other (OTH) AF: 0.529 AC: 1115 AN: 2108

Alfa AF: 0.604 Hom.: 40718

Bravo AF: 0.529

Asia WGS AF: 0.228 AC: 794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.58
DANN	Benign	0.55
PhyloP100		-0.14

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: rs952122;

hg19: chr3-153408662;