rs1554268

Variant names:

• chr2-22208238-C-T
• rs1554268
• ENST00000450551.1:n.200+2627G>A

Variant summary

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

The ENST00000450551.1(LINC01830):​n.200+2627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 151,878 control chromosomes in the GnomAD database, including 37,944 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 0.70 (37944 hom., cov: 31)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 3 publications found

Genes affected

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

ENSG00000310169 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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.200+2627G>A		intron_variant	Intron 2 of 4	5
ENSG00000310169	ENST00000847765.1	n.72+9389C>T		intron_variant	Intron 1 of 3
ENSG00000310169	ENST00000847766.1	n.73+9389C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105462 AN: 151760 Hom.: 37879 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.695 AC: 105585 AN: 151878 Hom.: 37944 Cov.: 31 AF XY: 0.702 AC XY: 52108 AN XY: 74206

African (AFR) AF: 0.847 AC: 35123 AN: 41464

American (AMR) AF: 0.758 AC: 11558 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1954 AN: 3468

East Asian (EAS) AF: 0.947 AC: 4856 AN: 5130

South Asian (SAS) AF: 0.810 AC: 3901 AN: 4814

European-Finnish (FIN) AF: 0.647 AC: 6826 AN: 10552

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39198 AN: 67892

Other (OTH) AF: 0.703 AC: 1482 AN: 2108

Alfa AF: 0.641 Hom.: 15291

Bravo AF: 0.709

Asia WGS AF: 0.878 AC: 3054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.62
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1554268; hg19: chr2-22431110;