18-64224173-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033881.1(LINC01924):n.201-25128C>G 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 0.649 in 152,046 control chromosomes in the GnomAD database, including 34,074 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 0.65 (34074 hom., cov: 32)
• Consequence: LINC01924 NR_033881.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

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

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01924	NR_033881.1	n.201-25128C>G		intron_variant, non_coding_transcript_variant
LINC01538	NR_033983.1	n.444-9127G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01538	ENST00000588074.1	n.444-9127G>C		intron_variant, non_coding_transcript_variant		1
LINC01924	ENST00000589376.1	n.201-25128C>G		intron_variant, non_coding_transcript_variant		1
LINC01538	ENST00000649058.1	n.383-31351G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98638 AN: 151928 Hom.: 34025 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.649 AC: 98742 AN: 152046 Hom.: 34074 Cov.: 32 AF XY: 0.647 AC XY: 48054 AN XY: 74308

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.509

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.626

Alfa AF: 0.418 Hom.: 999

Bravo AF: 0.668

Asia WGS AF: 0.657 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11876820; hg19: chr18-61891408;