chr10-3462838-A-G

Variant names:

• chr10-3462838-A-G
• rs1964428
• ENST00000659295.1:n.482-27860T>C

Variant summary

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

The ENST00000659295.1(LINC02669):​n.482-27860T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,024 control chromosomes in the GnomAD database, including 9,627 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 0.33 (9627 hom., cov: 32)
• Consequence: LINC02669 ENST00000659295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.162+143982A>G		intron_variant	Intron 1 of 1
LINC02669	NR_155743.1	n.632-27860T>C		intron_variant	Intron 3 of 4
LOC124902538	XR_007062362.1	n.3056+10149A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02669	ENST00000659295.1	n.482-27860T>C		intron_variant	Intron 3 of 4
LINC02669	ENST00000660786.1	n.645-27860T>C		intron_variant	Intron 3 of 4
LINC02669	ENST00000783314.1	n.305-9861T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50466 AN: 151906 Hom.: 9618 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.332 AC: 50505 AN: 152024 Hom.: 9627 Cov.: 32 AF XY: 0.334 AC XY: 24837 AN XY: 74326

African (AFR) AF: 0.506 AC: 20944 AN: 41394

American (AMR) AF: 0.328 AC: 5005 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2537 AN: 5172

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4824

European-Finnish (FIN) AF: 0.299 AC: 3163 AN: 10578

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15884 AN: 67994

Other (OTH) AF: 0.311 AC: 658 AN: 2114

Alfa AF: 0.265 Hom.: 23470

Bravo AF: 0.347

Asia WGS AF: 0.326 AC: 1135 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	0.29
DANN	Benign	0.52
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1964428; hg19: chr10-3505030;