12-73207352-C-T

Position:

• chr12-73207352-C-T

Variant summary

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

The NR_110130.1(LINC02444):​n.386-95C>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 0.201 in 151,912 control chromosomes in the GnomAD database, including 3,475 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 (3474 hom., cov: 31)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: LINC02444 NR_110130.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

LINC02444 (HGNC:53376): (long intergenic non-protein coding RNA 2444)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02444	NR_110130.1	n.386-95C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02444	ENST00000550723.1	n.386-95C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30509 AN: 151776 Hom.: 3473 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.333 AC: 6 AN: 18 Hom.: 1 AF XY: 0.286 AC XY: 4 AN XY: 14

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.429

GnomAD4 genome AF: 0.201 AC: 30511 AN: 151894 Hom.: 3474 Cov.: 31 AF XY: 0.201 AC XY: 14886 AN XY: 74238

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.204

Alfa AF: 0.245 Hom.: 9831

Bravo AF: 0.187

Asia WGS AF: 0.166 AC: 576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11615274; hg19: chr12-73601132;