10-62299502-C-T

Variant names:

• chr10-62299502-C-T
• rs6479805
• ENST00000442753.1:n.128-2824C>T

Variant summary

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

The ENST00000442753.1(LINC02621):​n.128-2824C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02621	NR_186389.1	n.213-2824C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02621	ENST00000442753.1	n.128-2824C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.332 AC: 13712 AN: 41324

American (AMR) AF: 0.678 AC: 10339 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2454 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4725 AN: 5136

South Asian (SAS) AF: 0.512 AC: 2460 AN: 4806

European-Finnish (FIN) AF: 0.764 AC: 8070 AN: 10558

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.661 AC: 44901 AN: 67910

Other (OTH) AF: 0.600 AC: 1263 AN: 2104

Alfa AF: 0.643 Hom.: 135778

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6479805; hg19: chr10-64059261;