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. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649298.1. 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
	LINC01924	ENST00000649298.1		n.675+11644G>A		intron	N/A
	LINC01924	ENST00000844483.1		n.25+8211G>A		intron	N/A

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

African (AFR) AF: 0.853 AC: 35287 AN: 41364

American (AMR) AF: 0.888 AC: 13543 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3470

East Asian (EAS) AF: 0.916 AC: 4704 AN: 5134

South Asian (SAS) AF: 0.886 AC: 4258 AN: 4804

European-Finnish (FIN) AF: 0.786 AC: 8252 AN: 10498

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56224 AN: 67956

Other (OTH) AF: 0.846 AC: 1782 AN: 2106

Alfa AF: 0.831 Hom.: 6805

Bravo AF: 0.853

Asia WGS AF: 0.917 AC: 3186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.52
PhyloP100		0.38

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: rs213090;

hg19: chr18-61721107;