rs213090

Variant names:

• chr18-64053873-G-A
• rs213090
• ENST00000649298.1:n.675+11644G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-64053873-G-A
• chr18-64053873-G-C

Variant summary

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

The ENST00000649298.1(LINC01924):​n.675+11644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 151,782 control chromosomes in the GnomAD database, including 54,105 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 0.84 (54105 hom., cov: 28)
• Consequence: LINC01924 ENST00000649298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378

Genes affected

LINC01924 (HGNC:27600): (long intergenic non-protein coding RNA 1924)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 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
LINC01924	ENST00000649298.1	n.675+11644G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128028 AN: 151664 Hom.: 54068 Cov.: 28

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.844 AC: 128119 AN: 151782 Hom.: 54105 Cov.: 28 AF XY: 0.846 AC XY: 62714 AN XY: 74166

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.888

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.846

Alfa AF: 0.830 Hom.: 6524

Bravo AF: 0.853

Asia WGS AF: 0.917 AC: 3186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs213090; hg19: chr18-61721107;