rs2033838

Variant names:

• chr2-188004033-G-A
• rs2033838
• ENST00000434418.2:n.496+31563C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-188004033-G-A
• chr2-188004033-G-C
• chr2-188004033-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434418.2(LINC01090):​n.496+31563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,066 control chromosomes in the GnomAD database, including 44,292 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 0.75 (44292 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 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
LINC01090	ENST00000434418.2	n.496+31563C>T		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113792 AN: 151948 Hom.: 44288 Cov.: 32

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.834

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.749 AC: 113835 AN: 152066 Hom.: 44292 Cov.: 32 AF XY: 0.753 AC XY: 55990 AN XY: 74340

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.890

Gnomad4 FIN AF: 0.834

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.773

Alfa AF: 0.816 Hom.: 23252

Bravo AF: 0.733

Asia WGS AF: 0.853 AC: 2963 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.55
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2033838; hg19: chr2-188868760;