rs2165468

Variant names:

• chr10-3473913-C-A
• rs2165468
• ENST00000659295.1:n.481+23740G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-3473913-C-A
• chr10-3473913-C-G
• chr10-3473913-C-T

Variant summary

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

The ENST00000659295.1(LINC02669):​n.481+23740G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,024 control chromosomes in the GnomAD database, including 3,748 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 0.20 (3748 hom., cov: 32)
• Consequence: LINC02669 ENST00000659295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+155057C>A		intron_variant	Intron 1 of 1
LINC02669	NR_155743.1	n.631+23740G>T		intron_variant	Intron 3 of 4
LOC124902538	XR_007062362.1	n.3056+21224C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02669	ENST00000659295.1	n.481+23740G>T		intron_variant	Intron 3 of 4
LINC02669	ENST00000660786.1	n.644+23740G>T		intron_variant	Intron 3 of 4
LINC02669	ENST00000783314.1	n.305-20936G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30491 AN: 151906 Hom.: 3747 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.201 AC: 30505 AN: 152024 Hom.: 3748 Cov.: 32 AF XY: 0.210 AC XY: 15572 AN XY: 74286

African (AFR) AF: 0.283 AC: 11706 AN: 41432

American (AMR) AF: 0.253 AC: 3875 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 484 AN: 3470

East Asian (EAS) AF: 0.469 AC: 2420 AN: 5160

South Asian (SAS) AF: 0.183 AC: 883 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2590 AN: 10558

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7883 AN: 67978

Other (OTH) AF: 0.179 AC: 377 AN: 2110

Alfa AF: 0.151 Hom.: 6885

Bravo AF: 0.208

Asia WGS AF: 0.272 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.55
DANN	Benign	0.48
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2165468; hg19: chr10-3516105;