rs1435867

chr2-228646213-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+98430A>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 0.0743 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01807	ENST00000665053.1	n.125+98430A>G		intron_variant, non_coding_transcript_variant
LINC01807	ENST00000667233.1	n.365+98430A>G		intron_variant, non_coding_transcript_variant

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;