rs1358443

Positions:

• chr2-228717688-T-C

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01807	ENST00000665053.1	n.125+26955A>G		intron_variant, non_coding_transcript_variant
LINC01807	ENST00000667233.1	n.365+26955A>G		intron_variant, non_coding_transcript_variant

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;