chr2-186032920-G-A

Position:

• chr2-186032920-G-A

Variant summary

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

The ENST00000456653.6(LINC01473):​n.1050C>T 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 0.67 in 149,984 control chromosomes in the GnomAD database, including 33,773 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 0.67 (33773 hom., cov: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01473 ENST00000456653.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690

Genes affected

LINC01473 (HGNC:51109): (long intergenic non-protein coding RNA 1473)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01473	ENST00000456653.6	n.1050C>T		non_coding_transcript_exon_variant	3/3	3
LINC01473	ENST00000655126.1	n.1422C>T		non_coding_transcript_exon_variant	9/9
LINC01473	ENST00000656786.1	n.1089C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.670 AC: 100460 AN: 149894 Hom.: 33761 Cov.: 27

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.674

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.670 AC: 100504 AN: 149984 Hom.: 33773 Cov.: 27 AF XY: 0.663 AC XY: 48426 AN XY: 73084

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.668

Alfa AF: 0.667 Hom.: 4023

Bravo AF: 0.669

Asia WGS AF: 0.557 AC: 1929 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878845; hg19: chr2-186897647;