ENST00000665053.1:n.125+98430A>G

Variant names:

• chr2-228646213-T-C
• rs1435867
• ENST00000665053.1:n.125+98430A>G

Variant summary

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

The ENST00000665053.1(LINC01807):​n.125+98430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0743 in 152,128 control chromosomes in the GnomAD database, including 440 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 0.074 (440 hom., cov: 32)
• Consequence: LINC01807 ENST00000665053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 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+98430A>G		intron_variant	Intron 2 of 5
LINC01807	ENST00000667233.1	n.365+98430A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11268 AN: 152010 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0405

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0743 AC: 11299 AN: 152128 Hom.: 440 Cov.: 32 AF XY: 0.0750 AC XY: 5579 AN XY: 74376

Gnomad4 AFR AF: 0.0688

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0505

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0405

Gnomad4 NFE AF: 0.0722

Gnomad4 OTH AF: 0.0730

Alfa AF: 0.0719 Hom.: 528

Bravo AF: 0.0759

Asia WGS AF: 0.145 AC: 500 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1435867; hg19: chr2-229510929;