rs1358443

Variant names:

• chr2-228717688-T-C
• rs1358443
• ENST00000665053.1:n.125+26955A>G

Variant summary

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

The ENST00000665053.1(LINC01807):​n.125+26955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,986 control chromosomes in the GnomAD database, including 2,189 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 0.17 (2189 hom., cov: 32)
• Consequence: LINC01807 ENST00000665053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

LINC01807 (HGNC:52610): (long intergenic non-protein coding RNA 1807)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 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
LINC01807	ENST00000665053.1	n.125+26955A>G		intron_variant	Intron 2 of 5
LINC01807	ENST00000667233.1	n.365+26955A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25108 AN: 151868 Hom.: 2182 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.165 AC: 25136 AN: 151986 Hom.: 2189 Cov.: 32 AF XY: 0.166 AC XY: 12319 AN XY: 74298

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.166

Alfa AF: 0.173 Hom.: 1411

Bravo AF: 0.164

Asia WGS AF: 0.250 AC: 862 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358443; hg19: chr2-229582404;