10-62299502-C-T

Position:

• chr10-62299502-C-T

Variant summary

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

The ENST00000442753.1(LINC02621):​n.128-2824C>T 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 0.584 in 151,768 control chromosomes in the GnomAD database, including 28,065 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 0.58 (28065 hom., cov: 30)
• Consequence: LINC02621 ENST00000442753.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

Genes affected

LINC02621 (HGNC:54098): (long intergenic non-protein coding RNA 2621)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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
LINC02621	ENST00000442753.1	n.128-2824C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88582 AN: 151648 Hom.: 28066 Cov.: 30

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.584 AC: 88603 AN: 151768 Hom.: 28065 Cov.: 30 AF XY: 0.591 AC XY: 43836 AN XY: 74152

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.600

Alfa AF: 0.655 Hom.: 66814

Bravo AF: 0.574

Asia WGS AF: 0.688 AC: 2393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6479805; hg19: chr10-64059261;