rs1997325

Variant names:

• chr2-22600878-C-T
• rs1997325
• ENST00000833262.1:n.194-25156G>A

Variant summary

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

The ENST00000833262.1(LINC01830):​n.194-25156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,160 control chromosomes in the GnomAD database, including 52,434 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 0.83 (52434 hom., cov: 33)
• Consequence: LINC01830 ENST00000833262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.901 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.194-25156G>A		intron_variant	Intron 2 of 5
LINC01830	ENST00000833263.1	n.211+29061G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125998 AN: 152042 Hom.: 52387 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.829 AC: 126101 AN: 152160 Hom.: 52434 Cov.: 33 AF XY: 0.829 AC XY: 61631 AN XY: 74368

African (AFR) AF: 0.785 AC: 32573 AN: 41492

American (AMR) AF: 0.764 AC: 11677 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.889 AC: 3084 AN: 3470

East Asian (EAS) AF: 0.881 AC: 4542 AN: 5154

South Asian (SAS) AF: 0.924 AC: 4463 AN: 4830

European-Finnish (FIN) AF: 0.851 AC: 9018 AN: 10592

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.851 AC: 57907 AN: 68014

Other (OTH) AF: 0.839 AC: 1776 AN: 2116

Alfa AF: 0.844 Hom.: 67454

Bravo AF: 0.817

Asia WGS AF: 0.885 AC: 3063 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.62
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1997325; hg19: chr2-22823750;