rs1274409

Variant names:

• chr10-90603040-C-T
• rs1274409
• ENST00000660339.2:n.212+25730G>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+25730G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,142 control chromosomes in the GnomAD database, including 4,503 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 0.24 (4503 hom., cov: 33)
• Consequence: LINC02653 ENST00000660339.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 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+25730G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36490 AN: 152024 Hom.: 4504 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.240 AC: 36522 AN: 152142 Hom.: 4503 Cov.: 33 AF XY: 0.241 AC XY: 17909 AN XY: 74346

African (AFR) AF: 0.234 AC: 9723 AN: 41500

American (AMR) AF: 0.184 AC: 2813 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3470

East Asian (EAS) AF: 0.257 AC: 1331 AN: 5174

South Asian (SAS) AF: 0.172 AC: 827 AN: 4822

European-Finnish (FIN) AF: 0.338 AC: 3577 AN: 10578

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16603 AN: 67984

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.237 Hom.: 5715

Bravo AF: 0.228

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.65
DANN	Benign	0.41
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1274409; hg19: chr10-92362797;