rs10498230

chr2-228637787-C-T

Variant summary

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

The ENST00000665053.1(LINC01807):n.125+106856G>A 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 0.0741 in 152,158 control chromosomes in the GnomAD database, including 437 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 (437 hom., cov: 32)
• Consequence: LINC01807 ENST00000665053.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 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+106856G>A		intron_variant, non_coding_transcript_variant
LINC01807	ENST00000667233.1	n.365+106856G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 11238 AN: 152040 Hom.: 428 Cov.: 32

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.0505

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0662

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

GnomAD4 genome AF: 0.0741 AC: 11268 AN: 152158 Hom.: 437 Cov.: 32 AF XY: 0.0748 AC XY: 5564 AN XY: 74372

Gnomad4 AFR AF: 0.0677

Gnomad4 AMR AF: 0.0865

Gnomad4 ASJ AF: 0.0505

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0723

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0740 Hom.: 91

Bravo AF: 0.0756

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498230; hg19: chr2-229502503;