rs2046593

Positions:

• chr2-186079936-C-A
• chr2-186079936-C-G
• chr2-186079936-C-T

Variant summary

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

The NR_110218.1(LINC01473):​n.172+1394G>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 0.825 in 151,964 control chromosomes in the GnomAD database, including 51,831 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 0.83 (51831 hom., cov: 31)
• Consequence: LINC01473 NR_110218.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01473	NR_110218.1	n.172+1394G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01473	ENST00000703419.1	n.556+1394G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125323 AN: 151846 Hom.: 51789 Cov.: 31

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.833

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.825 AC: 125415 AN: 151964 Hom.: 51831 Cov.: 31 AF XY: 0.822 AC XY: 61059 AN XY: 74244

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.830

Alfa AF: 0.814 Hom.: 19649

Bravo AF: 0.835

Asia WGS AF: 0.864 AC: 3004 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2046593; hg19: chr2-186944663;