18-64418271-G-A

Variant names:

• chr18-64418271-G-A
• rs1421521
• ENST00000589376.1:n.977+2160G>A

Variant summary

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

The ENST00000589376.1(LINC01924):​n.977+2160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,418 control chromosomes in the GnomAD database, including 7,048 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 0.28 (7048 hom., cov: 32)
• Consequence: LINC01924 ENST00000589376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589376.1. 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
	LINC01924	NR_033881.1		n.977+2160G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01924	ENST00000589376.1	TSL:1	n.977+2160G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41910 AN: 151304 Hom.: 7053 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.277 AC: 41894 AN: 151418 Hom.: 7048 Cov.: 32 AF XY: 0.283 AC XY: 20899 AN XY: 73968

African (AFR) AF: 0.0658 AC: 2725 AN: 41416

American (AMR) AF: 0.419 AC: 6370 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3464

East Asian (EAS) AF: 0.359 AC: 1842 AN: 5124

South Asian (SAS) AF: 0.350 AC: 1669 AN: 4766

European-Finnish (FIN) AF: 0.337 AC: 3533 AN: 10472

Middle Eastern (MID) AF: 0.417 AC: 121 AN: 290

European-Non Finnish (NFE) AF: 0.345 AC: 23350 AN: 67684

Other (OTH) AF: 0.310 AC: 652 AN: 2106

Alfa AF: 0.252 Hom.: 2697

Bravo AF: 0.276

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs1421521; hg19: chr18-62085506;