rs4534959

Variant names:

• chr18-64209921-A-G
• rs4534959
• ENST00000589376.1:n.201-39380A>G

Variant summary

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

The ENST00000589376.1(LINC01924):​n.201-39380A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,200 control chromosomes in the GnomAD database, including 263 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 0.044 (263 hom., cov: 32)
• Consequence: LINC01924 ENST00000589376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128
• Publications: 3 publications found

Genes affected

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

LINC01538 (HGNC:51306): (long intergenic non-protein coding RNA 1538)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01924	NR_033881.1	n.201-39380A>G		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01924	ENST00000589376.1	n.201-39380A>G		intron_variant	Intron 2 of 9	1
LINC01538	ENST00000649058.1	n.383-17099T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6735 AN: 152082 Hom.: 265 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0505

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0350

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0442 AC: 6731 AN: 152200 Hom.: 263 Cov.: 32 AF XY: 0.0486 AC XY: 3612 AN XY: 74386

African (AFR) AF: 0.0241 AC: 1002 AN: 41552

American (AMR) AF: 0.0507 AC: 775 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.192 AC: 991 AN: 5168

South Asian (SAS) AF: 0.0344 AC: 166 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10566

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0333 AC: 2263 AN: 68010

Other (OTH) AF: 0.0407 AC: 86 AN: 2114

Alfa AF: 0.0391 Hom.: 315

Bravo AF: 0.0399

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	10
DANN	Benign	0.50
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4534959; hg19: chr18-61877156;