10-3496602-A-C

Variant names:

• chr10-3496602-A-C
• rs7092929
• ENST00000413993.2:n.709-366T>G

Variant summary

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

The ENST00000413993.2(LINC02669):​n.709-366T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,926 control chromosomes in the GnomAD database, including 45,196 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 0.76 (45196 hom., cov: 31)
• Consequence: LINC02669 ENST00000413993.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 9 publications found

Genes affected

LINC02669 (HGNC:54155): (long intergenic non-protein coding RNA 2669)

ENSG00000286610 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+177746A>C		intron_variant	Intron 1 of 1
LINC02669	NR_155743.1	n.631+1051T>G		intron_variant	Intron 3 of 4
LINC02669	NR_155744.1	n.632-4T>G		splice_region_variant, intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02669	ENST00000413993.2	n.709-366T>G		intron_variant	Intron 3 of 4	3
LINC02669	ENST00000655104.1	n.413+1051T>G		intron_variant	Intron 3 of 3
LINC02669	ENST00000656403.1	n.548-4T>G		splice_region_variant, intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116137 AN: 151808 Hom.: 45183 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.765 AC: 116195 AN: 151926 Hom.: 45196 Cov.: 31 AF XY: 0.755 AC XY: 56108 AN XY: 74272

African (AFR) AF: 0.742 AC: 30720 AN: 41396

American (AMR) AF: 0.696 AC: 10603 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2937 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2057 AN: 5158

South Asian (SAS) AF: 0.654 AC: 3152 AN: 4822

European-Finnish (FIN) AF: 0.725 AC: 7652 AN: 10548

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56674 AN: 67980

Other (OTH) AF: 0.785 AC: 1654 AN: 2108

Alfa AF: 0.795 Hom.: 29777

Bravo AF: 0.761

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.46
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs7092929; hg19: chr10-3538794;