ENST00000450551.1:n.71-134847T>A

Variant names:

• chr2-22345841-A-T
• rs7569716
• ENST00000450551.1:n.71-134847T>A

Variant summary

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

The ENST00000450551.1(LINC01830):​n.71-134847T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 149,192 control chromosomes in the GnomAD database, including 4,055 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 0.21 (4055 hom., cov: 33)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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.71-134847T>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.207 AC: 30905 AN: 149100 Hom.: 4047 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.207 AC: 30945 AN: 149192 Hom.: 4055 Cov.: 33 AF XY: 0.208 AC XY: 15191 AN XY: 72962

African (AFR) AF: 0.381 AC: 14794 AN: 38808

American (AMR) AF: 0.253 AC: 3813 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 857 AN: 3470

East Asian (EAS) AF: 0.145 AC: 749 AN: 5166

South Asian (SAS) AF: 0.136 AC: 659 AN: 4828

European-Finnish (FIN) AF: 0.123 AC: 1308 AN: 10600

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.119 AC: 8102 AN: 67964

Other (OTH) AF: 0.213 AC: 443 AN: 2076

Alfa AF: 0.167 Hom.: 362

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7569716; hg19: chr2-22568713;