2-22689630-G-C

Variant names:

• chr2-22689630-G-C
• rs3893249
• ENST00000833262.1:n.100+5135C>G

Variant summary

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

The ENST00000833262.1(LINC01830):​n.100+5135C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 151,922 control chromosomes in the GnomAD database, including 626 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 0.091 (626 hom., cov: 32)
• Consequence: LINC01830 ENST00000833262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833262.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01830	ENST00000833262.1		n.100+5135C>G		intron	N/A
	LINC01830	ENST00000833263.1		n.118+5135C>G		intron	N/A
	LINC01830	ENST00000833264.1		n.577-2762C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0909 AC: 13800 AN: 151804 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.0826

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.0909 AC: 13807 AN: 151922 Hom.: 626 Cov.: 32 AF XY: 0.0931 AC XY: 6910 AN XY: 74244

African (AFR) AF: 0.128 AC: 5307 AN: 41450

American (AMR) AF: 0.0570 AC: 870 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3468

East Asian (EAS) AF: 0.0822 AC: 421 AN: 5124

South Asian (SAS) AF: 0.105 AC: 507 AN: 4806

European-Finnish (FIN) AF: 0.111 AC: 1169 AN: 10550

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5011 AN: 67954

Other (OTH) AF: 0.0787 AC: 166 AN: 2110

Alfa AF: 0.0357 Hom.: 26

Bravo AF: 0.0864

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.59
PhyloP100		2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3893249;

hg19: chr2-22912502;