3-153935638-T-C

Position:

• chr3-153935638-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000488210.1(LINC02006):​n.420+1870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,874 control chromosomes in the GnomAD database, including 31,729 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 0.63 (31729 hom., cov: 31)
• Consequence: LINC02006 ENST00000488210.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

Genes affected

ENSG00000243486 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000243486	ENST00000463297.1	n.209+578T>C		intron_variant		5
LINC02006	ENST00000488210.1	n.420+1870A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96012 AN: 151756 Hom.: 31728 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.632 AC: 96045 AN: 151874 Hom.: 31729 Cov.: 31 AF XY: 0.636 AC XY: 47221 AN XY: 74206

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.640

Alfa AF: 0.675 Hom.: 18266

Bravo AF: 0.626

Asia WGS AF: 0.749 AC: 2602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10935960; hg19: chr3-153653427;