rs7970012

chr12-126874646-T-Cchr12-126874646-T-G

Variant summary

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

The NR_033970.1(LINC02372):n.45A>G 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 0.237 in 152,262 control chromosomes in the GnomAD database, including 5,420 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 0.24 (5418 hom., cov: 32)
  • Exomes 𝑓: 0.25 (2 hom.)
• Consequence: LINC02372 NR_033970.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

LINC02372 (HGNC:53294): (long intergenic non-protein coding RNA 2372)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02372	NR_033970.1	n.45A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02372	ENST00000654468.1	n.80A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36104 AN: 152108 Hom.: 5418 Cov.: 32

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.250 AC: 9 AN: 36 Hom.: 2 Cov.: 0 AF XY: 0.267 AC XY: 8 AN XY: 30

Gnomad4 ASJ exome AF: 1.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.214

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.237 AC: 36093 AN: 152226 Hom.: 5418 Cov.: 32 AF XY: 0.237 AC XY: 17631 AN XY: 74424

Gnomad4 AFR AF: 0.0784

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.272

Alfa AF: 0.314 Hom.: 6557

Bravo AF: 0.221

Asia WGS AF: 0.124 AC: 431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.5
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7970012; hg19: chr12-127359192;