12-47837827-A-G

Position:

• chr12-47837827-A-G

Variant summary

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

The XR_007063292.1(LINC02354):​n.797A>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 0.451 in 152,034 control chromosomes in the GnomAD database, including 15,867 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 0.45 (15866 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: LINC02354 XR_007063292.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

LINC02354 (HGNC:53276): (long intergenic non-protein coding RNA 2354)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02354	XR_007063292.1	n.797A>G		non_coding_transcript_exon_variant	3/3
LINC02354	XR_001749114.2	n.528A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02354	ENST00000548564.1	n.502A>G		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68531 AN: 151910 Hom.: 15859 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.454

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.750

GnomAD4 genome AF: 0.451 AC: 68573 AN: 152028 Hom.: 15866 Cov.: 32 AF XY: 0.450 AC XY: 33455 AN XY: 74316

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.453

Alfa AF: 0.382 Hom.: 1882

Bravo AF: 0.439

Asia WGS AF: 0.356 AC: 1238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7965281; hg19: chr12-48231610;