ENST00000450551.1:n.71-142234T>C

Variant names:

• chr2-22353228-A-G
• rs1605834
• ENST00000450551.1:n.71-142234T>C

Variant summary

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

The ENST00000450551.1(LINC01830):​n.71-142234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,482 control chromosomes in the GnomAD database, including 6,733 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 0.25 (6733 hom., cov: 29)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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	ENST00000450551.1	n.71-142234T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38428 AN: 151368 Hom.: 6710 Cov.: 29

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.254 AC: 38505 AN: 151482 Hom.: 6733 Cov.: 29 AF XY: 0.251 AC XY: 18610 AN XY: 74008

African (AFR) AF: 0.490 AC: 20164 AN: 41144

American (AMR) AF: 0.277 AC: 4192 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3470

East Asian (EAS) AF: 0.162 AC: 835 AN: 5158

South Asian (SAS) AF: 0.0949 AC: 455 AN: 4794

European-Finnish (FIN) AF: 0.136 AC: 1428 AN: 10536

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9834 AN: 67910

Other (OTH) AF: 0.249 AC: 524 AN: 2104

Alfa AF: 0.179 Hom.: 13612

Bravo AF: 0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.95
DANN	Benign	0.55
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1605834; hg19: chr2-22576100;