3-153760634-G-C

Variant names:

• chr3-153760634-G-C
• rs6794649
• ENST00000488210.1:n.478-29827C>G

Variant summary

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

The ENST00000493214.2(LINC02006):​n.24+1869C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,990 control chromosomes in the GnomAD database, including 2,303 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 0.17 (2303 hom., cov: 32)
• Consequence: LINC02006 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02006	NR_146713.1	n.24+1869C>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02006	ENST00000488210.1	n.478-29827C>G		intron_variant	Intron 3 of 3	4
LINC02006	ENST00000493214.2	n.24+1869C>G		intron_variant	Intron 1 of 6	2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25068 AN: 151872 Hom.: 2298 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.165 AC: 25107 AN: 151990 Hom.: 2303 Cov.: 32 AF XY: 0.172 AC XY: 12768 AN XY: 74280

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.169

Alfa AF: 0.0963 Hom.: 153

Bravo AF: 0.160

Asia WGS AF: 0.286 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6794649; hg19: chr3-153478423;