chr18-64171222-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01924	NR_033881.1	n.200+43783C>G		intron_variant	Intron 2 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01924	ENST00000589376.1	n.200+43783C>G		intron_variant	Intron 2 of 9	1

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

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.299

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944328; hg19: chr18-61838457;