ENST00000833262.1:n.194-23565C>T

Variant names:

• chr2-22599287-G-A
• rs13015955
• ENST00000833262.1:n.194-23565C>T

Variant summary

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

The ENST00000833262.1(LINC01830):​n.194-23565C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,056 control chromosomes in the GnomAD database, including 3,141 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 0.18 (3141 hom., cov: 32)
• Consequence: LINC01830 ENST00000833262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498
• Publications: 12 publications found

Genes affected

LINC01830 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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
LINC01830	ENST00000833262.1	n.194-23565C>T		intron_variant	Intron 2 of 5
LINC01830	ENST00000833263.1	n.211+30652C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26720 AN: 151938 Hom.: 3140 Cov.: 32

Gnomad AFR AF: 0.0444

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0888

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.176 AC: 26723 AN: 152056 Hom.: 3141 Cov.: 32 AF XY: 0.171 AC XY: 12690 AN XY: 74324

African (AFR) AF: 0.0443 AC: 1837 AN: 41488

American (AMR) AF: 0.166 AC: 2542 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0893 AC: 429 AN: 4802

European-Finnish (FIN) AF: 0.222 AC: 2348 AN: 10568

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17853 AN: 67954

Other (OTH) AF: 0.179 AC: 379 AN: 2114

Alfa AF: 0.222 Hom.: 8830

Bravo AF: 0.167

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs13015955; hg19: chr2-22822159;