rs13020676

Variant names:

• chr2-22003535-G-A
• rs13020676
• ENST00000450551.1:n.201-31699C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-22003535-G-A
• chr2-22003535-G-T

Variant summary

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

The ENST00000450551.1(LINC01830):​n.201-31699C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.23 (3170 hom., cov: 20)
• Consequence: LINC01830 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• 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=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01830	ENST00000450551.1	TSL:5	n.201-31699C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 27081 AN: 117050 Hom.: 3168 Cov.: 20

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.231 AC: 27082 AN: 117080 Hom.: 3170 Cov.: 20 AF XY: 0.232 AC XY: 12681 AN XY: 54758

African (AFR) AF: 0.123 AC: 3558 AN: 28848

American (AMR) AF: 0.237 AC: 2229 AN: 9406

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 980 AN: 3244

East Asian (EAS) AF: 0.0115 AC: 40 AN: 3464

South Asian (SAS) AF: 0.205 AC: 707 AN: 3446

European-Finnish (FIN) AF: 0.290 AC: 1403 AN: 4830

Middle Eastern (MID) AF: 0.294 AC: 50 AN: 170

European-Non Finnish (NFE) AF: 0.286 AC: 17511 AN: 61290

Other (OTH) AF: 0.244 AC: 382 AN: 1568

Alfa AF: 0.225 Hom.: 7608

Bravo AF: 0.185

Asia WGS AF: 0.0780 AC: 272 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs13020676; hg19: chr2-22226407;