2-186349003-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01473	ENST00000667056.1	n.104+73326A>G		intron_variant	Intron 1 of 9
LINC01473	ENST00000671599.1	n.104+73326A>G		intron_variant	Intron 1 of 6
LINC01473	ENST00000703419.1	n.344-43784A>G		intron_variant	Intron 2 of 7

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.181

Alfa AF: 0.179 Hom.: 2744

Bravo AF: 0.164

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497668; hg19: chr2-187213730;