10-101258564-C-T

Position:

• chr10-101258564-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02681	NR_120621.1	n.475+2303G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02681	ENST00000422661.1	n.475+2303G>A		intron_variant		2
LBX1-AS1	ENST00000434878.1	n.111-9008C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.0615

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0462

Gnomad4 SAS AF: 0.0968

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.195

Alfa AF: 0.268 Hom.: 6863

Bravo AF: 0.185

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17686462; hg19: chr10-103018321;