10-90603040-C-T

Position:

• chr10-90603040-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660339.1(LINC02653):​n.83+25730G>A variant causes a intron, non coding transcript 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 ENST00000660339.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02653	ENST00000660339.1	n.83+25730G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.241

Alfa AF: 0.238 Hom.: 4454

Bravo AF: 0.228

Asia WGS AF: 0.253 AC: 881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1274409; hg19: chr10-92362797;