rs3849399

Variant names:

• chr2-22688855-T-C
• rs3849399
• ENST00000833262.1:n.100+5910A>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+5910A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,256 control chromosomes in the GnomAD database, including 373 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 0.072 (373 hom., cov: 32)
• Consequence: LINC01830 ENST00000833262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0982 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.100+5910A>G		intron_variant	Intron 1 of 5
LINC01830	ENST00000833263.1	n.118+5910A>G		intron_variant	Intron 1 of 4
LINC01830	ENST00000833264.1	n.577-1987A>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10970 AN: 152138 Hom.: 373 Cov.: 32

Gnomad AFR AF: 0.0628

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0495

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0721 AC: 10974 AN: 152256 Hom.: 373 Cov.: 32 AF XY: 0.0740 AC XY: 5511 AN XY: 74434

African (AFR) AF: 0.0628 AC: 2611 AN: 41566

American (AMR) AF: 0.0494 AC: 756 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3468

East Asian (EAS) AF: 0.0820 AC: 423 AN: 5158

South Asian (SAS) AF: 0.106 AC: 510 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1175 AN: 10610

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0737 AC: 5012 AN: 68022

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0729 Hom.: 798

Bravo AF: 0.0653

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.55
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs3849399; hg19: chr2-22911727;