rs213090

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01924	ENST00000649298.1	n.675+11644G>A		intron_variant, non_coding_transcript_variant

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;