18-64171222-C-G

Variant names:

• chr18-64171222-C-G
• rs1944328
• ENST00000589376.1:n.200+43783C>G

Variant summary

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

The ENST00000589376.1(LINC01924):​n.200+43783C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,032 control chromosomes in the GnomAD database, including 12,459 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 0.34 (12459 hom., cov: 33)
• Consequence: LINC01924 ENST00000589376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01924	NR_033881.1		n.200+43783C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01924	ENST00000589376.1	TSL:1	n.200+43783C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51004 AN: 151914 Hom.: 12424 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.336 AC: 51081 AN: 152032 Hom.: 12459 Cov.: 33 AF XY: 0.335 AC XY: 24868 AN XY: 74322

African (AFR) AF: 0.689 AC: 28574 AN: 41480

American (AMR) AF: 0.279 AC: 4255 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3466

East Asian (EAS) AF: 0.300 AC: 1548 AN: 5160

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4822

European-Finnish (FIN) AF: 0.201 AC: 2128 AN: 10582

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11934 AN: 67948

Other (OTH) AF: 0.299 AC: 630 AN: 2110

Alfa AF: 0.136 Hom.: 313

Bravo AF: 0.355

Asia WGS AF: 0.327 AC: 1137 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.46
PhyloP100		-1.1

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: rs1944328;

hg19: chr18-61838457;