rs10498230

Variant names:

• chr2-228637787-C-T
• rs10498230
• ENST00000665053.1:n.125+106856G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665053.1(LINC01807):​n.125+106856G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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+106856G>A		intron	N/A
	LINC01807	ENST00000667233.2		n.370+106856G>A		intron	N/A

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

African (AFR) AF: 0.0677 AC: 2812 AN: 41512

American (AMR) AF: 0.0865 AC: 1322 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0505 AC: 175 AN: 3468

East Asian (EAS) AF: 0.139 AC: 717 AN: 5160

South Asian (SAS) AF: 0.146 AC: 703 AN: 4820

European-Finnish (FIN) AF: 0.0412 AC: 436 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0723 AC: 4914 AN: 68006

Other (OTH) AF: 0.0716 AC: 151 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10498230; hg19: chr2-229502503;