10-83673233-A-T

Variant names:

• chr10-83673233-A-T
• rs3829142
• ENST00000441776.2:n.289T>A

Variant summary

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

The ENST00000441776.2(LINC02650):​n.289T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,116 control chromosomes in the GnomAD database, including 1,437 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 0.11 (1437 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC02650 ENST00000441776.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

LINC02650 (HGNC:54135): (long intergenic non-protein coding RNA 2650)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02650	NR_134317.1	n.256T>A		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02650	ENST00000441776.2	n.289T>A		non_coding_transcript_exon_variant	Exon 4 of 5	3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16225 AN: 151996 Hom.: 1435 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0346

Gnomad OTH AF: 0.104

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 AFR exome AF: 0.500

GnomAD4 genome AF: 0.107 AC: 16238 AN: 152114 Hom.: 1437 Cov.: 33 AF XY: 0.110 AC XY: 8146 AN XY: 74372

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0688 Hom.: 91

Bravo AF: 0.115

Asia WGS AF: 0.209 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3829142; hg19: chr10-85432989;