rs902432

Variant names:

• chr3-153580135-G-T
• rs902432
• ENST00000493214.2:n.260+24511C>A

Variant summary

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

The ENST00000493214.2(LINC02006):​n.260+24511C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,032 control chromosomes in the GnomAD database, including 9,467 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 0.34 (9467 hom., cov: 32)
• Consequence: LINC02006 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02006	NR_146713.1	n.260+24511C>A		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02006	ENST00000493214.2	n.260+24511C>A		intron_variant	Intron 4 of 6	2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51916 AN: 151914 Hom.: 9449 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.342 AC: 51957 AN: 152032 Hom.: 9467 Cov.: 32 AF XY: 0.344 AC XY: 25530 AN XY: 74296

African (AFR) AF: 0.210 AC: 8691 AN: 41474

American (AMR) AF: 0.364 AC: 5564 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1834 AN: 5168

South Asian (SAS) AF: 0.458 AC: 2208 AN: 4820

European-Finnish (FIN) AF: 0.387 AC: 4088 AN: 10568

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27019 AN: 67938

Other (OTH) AF: 0.353 AC: 746 AN: 2112

Alfa AF: 0.382 Hom.: 12178

Bravo AF: 0.330

Asia WGS AF: 0.416 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.47
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs902432; hg19: chr3-153297924;