rs1421521

chr18-64418271-G-Achr18-64418271-G-C

Variant summary

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

The NR_033881.1(LINC01924):n.977+2160G>A 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 0.277 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 NR_033881.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01924	NR_033881.1	n.977+2160G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01924	ENST00000589376.1	n.977+2160G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0658

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.310

Alfa AF: 0.317 Hom.: 1443

Bravo AF: 0.276

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421521; hg19: chr18-62085506;