chr2-186349003-T-C

Variant names:

• chr2-186349003-T-C
• rs10497668
• ENST00000667056.1:n.104+73326A>G

Variant summary

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

The ENST00000667056.1(LINC01473):​n.104+73326A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,078 control chromosomes in the GnomAD database, including 2,408 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 0.18 (2408 hom., cov: 32)
• Consequence: LINC01473 ENST00000667056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667056.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01473	ENST00000667056.1		n.104+73326A>G		intron	N/A
	LINC01473	ENST00000668985.2		n.405-43784A>G		intron	N/A
	LINC01473	ENST00000671599.1		n.104+73326A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26716 AN: 151960 Hom.: 2400 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.176 AC: 26718 AN: 152078 Hom.: 2408 Cov.: 32 AF XY: 0.179 AC XY: 13313 AN XY: 74352

African (AFR) AF: 0.156 AC: 6452 AN: 41470

American (AMR) AF: 0.138 AC: 2105 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 677 AN: 3470

East Asian (EAS) AF: 0.100 AC: 518 AN: 5182

South Asian (SAS) AF: 0.191 AC: 921 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2610 AN: 10574

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12869 AN: 67986

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.178 Hom.: 3167

Bravo AF: 0.164

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.84
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10497668; hg19: chr2-187213730;