rs1358443

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ENSG00000298114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665053.1. 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
	LINC01807	ENST00000665053.1		n.125+26955A>G		intron	N/A
	LINC01807	ENST00000667233.2		n.370+26955A>G		intron	N/A
	ENSG00000298114	ENST00000753083.1		n.474+961T>C		intron	N/A

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

African (AFR) AF: 0.143 AC: 5924 AN: 41472

American (AMR) AF: 0.148 AC: 2249 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3462

East Asian (EAS) AF: 0.279 AC: 1439 AN: 5162

South Asian (SAS) AF: 0.255 AC: 1231 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1487 AN: 10550

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11920 AN: 67958

Other (OTH) AF: 0.166 AC: 350 AN: 2108

Alfa AF: 0.172 Hom.: 1682

Bravo AF: 0.164

Asia WGS AF: 0.250 AC: 862 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.56
PhyloP100		0.30

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: rs1358443;

hg19: chr2-229582404;