rs2046593

Variant names:

• chr2-186079936-C-A
• rs2046593
• ENST00000419719.3:n.313+1394G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419719.3(LINC01473):​n.313+1394G>T variant causes a intron 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 ENST00000419719.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.817
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419719.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01473	NR_110218.1		n.172+1394G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01473	ENST00000419719.3	TSL:2	n.313+1394G>T		intron	N/A
	LINC01473	ENST00000427108.6	TSL:5	n.294+1394G>T		intron	N/A
	LINC01473	ENST00000456653.6	TSL:3	n.167+1394G>T		intron	N/A

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

African (AFR) AF: 0.807 AC: 33475 AN: 41494

American (AMR) AF: 0.887 AC: 13487 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2901 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4803 AN: 5146

South Asian (SAS) AF: 0.842 AC: 4059 AN: 4818

European-Finnish (FIN) AF: 0.770 AC: 8127 AN: 10556

Middle Eastern (MID) AF: 0.801 AC: 234 AN: 292

European-Non Finnish (NFE) AF: 0.821 AC: 55764 AN: 67954

Other (OTH) AF: 0.830 AC: 1753 AN: 2112

Alfa AF: 0.816 Hom.: 22550

Bravo AF: 0.835

Asia WGS AF: 0.864 AC: 3004 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		0.82

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2046593;

hg19: chr2-186944663;