chr10-101258564-C-T

Variant names:

• chr10-101258564-C-T
• rs17686462
• ENST00000422661.1:n.475+2303G>A

Variant summary

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

The ENST00000422661.1(LINC02681):​n.475+2303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,996 control chromosomes in the GnomAD database, including 4,101 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 0.20 (4101 hom., cov: 31)
• Consequence: LINC02681 ENST00000422661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 2 publications found

Genes affected

LINC02681 (HGNC:54175): (long intergenic non-protein coding RNA 2681)

LBX1-AS1 (HGNC:48678): (LBX1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422661.1. 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
	LINC02681	NR_120621.1		n.475+2303G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02681	ENST00000422661.1	TSL:2	n.475+2303G>A		intron	N/A
	LBX1-AS1	ENST00000434878.1	TSL:5	n.111-9008C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30740 AN: 151878 Hom.: 4099 Cov.: 31

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30737 AN: 151996 Hom.: 4101 Cov.: 31 AF XY: 0.200 AC XY: 14874 AN XY: 74278

African (AFR) AF: 0.0615 AC: 2550 AN: 41486

American (AMR) AF: 0.166 AC: 2541 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3466

East Asian (EAS) AF: 0.0462 AC: 239 AN: 5176

South Asian (SAS) AF: 0.0968 AC: 465 AN: 4804

European-Finnish (FIN) AF: 0.306 AC: 3214 AN: 10510

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20417 AN: 67970

Other (OTH) AF: 0.195 AC: 412 AN: 2116

Alfa AF: 0.260 Hom.: 8444

Bravo AF: 0.185

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs17686462; hg19: chr10-103018321;