rs10861038

Positions:

• chr12-103559279-C-A
• chr12-103559279-C-T

Variant summary

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

The NR_110103.1(LINC02401):​n.2523C>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 0.0851 in 120,636 control chromosomes in the GnomAD database, including 390 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 0.085 (390 hom., cov: 30)
  • Exomes 𝑓: 0.036 (0 hom.)
• Consequence: LINC02401 NR_110103.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

LINC02401 (HGNC:53328): (long intergenic non-protein coding RNA 2401)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02401	NR_110103.1	n.2523C>A		non_coding_transcript_exon_variant	5/5
C12orf42	XM_047428803.1	c.-22+4368G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650784.1	n.204+4368G>T		intron_variant, non_coding_transcript_variant
LINC02401	ENST00000666598.1	n.491+1683C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 10262 AN: 120488 Hom.: 387 Cov.: 30

Gnomad AFR AF: 0.0726

Gnomad AMI AF: 0.0575

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0713

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0939

GnomAD4 exome AF: 0.0357 AC: 1 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.0455 AC XY: 1 AN XY: 22

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0455

GnomAD4 genome AF: 0.0851 AC: 10267 AN: 120608 Hom.: 390 Cov.: 30 AF XY: 0.0861 AC XY: 5066 AN XY: 58816

Gnomad4 AFR AF: 0.0727

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0711

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0897

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0641 Hom.: 478

Bravo AF: 0.0690

Asia WGS AF: 0.0860 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861038; hg19: chr12-103953057;