10-90603446-C-T

Variant names:

• chr10-90603446-C-T
• rs1779941
• ENST00000660339.2:n.212+25324G>A

Variant summary

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

The ENST00000660339.2(LINC02653):​n.212+25324G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,940 control chromosomes in the GnomAD database, including 21,022 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 0.52 (21022 hom., cov: 32)
• Consequence: LINC02653 ENST00000660339.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 1 publications found

Genes affected

LINC02653 (HGNC:54138): (long intergenic non-protein coding RNA 2653)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660339.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02653	ENST00000660339.2		n.212+25324G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79161 AN: 151822 Hom.: 21012 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.521 AC: 79222 AN: 151940 Hom.: 21022 Cov.: 32 AF XY: 0.515 AC XY: 38231 AN XY: 74254

African (AFR) AF: 0.476 AC: 19752 AN: 41460

American (AMR) AF: 0.483 AC: 7377 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3468

East Asian (EAS) AF: 0.259 AC: 1336 AN: 5150

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4816

European-Finnish (FIN) AF: 0.562 AC: 5927 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39313 AN: 67922

Other (OTH) AF: 0.503 AC: 1060 AN: 2106

Alfa AF: 0.420 Hom.: 1233

Bravo AF: 0.515

Asia WGS AF: 0.361 AC: 1256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.9
DANN	Benign	0.83
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs1779941; hg19: chr10-92363203;