rs1424401

Positions:

• chr18-55973548-G-A
• chr18-55973548-G-C

Variant summary

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

The ENST00000589440.1(LINC03092):​n.406-44180G>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 0.585 in 151,844 control chromosomes in the GnomAD database, including 27,075 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 0.58 (27075 hom., cov: 31)
• Consequence: LINC03092 ENST00000589440.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

LINC03092 (HGNC:56721): (long intergenic non-protein coding RNA 3092)

LINC01416 (HGNC:51645): (long intergenic non-protein coding RNA 1416)

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 (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03092	ENST00000589440.1	n.406-44180G>A		intron_variant, non_coding_transcript_variant		2
LINC01416	ENST00000654280.1	n.1512+23160C>T		intron_variant, non_coding_transcript_variant
LINC01416	ENST00000655696.1	n.1303+23160C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88686 AN: 151726 Hom.: 27043 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.585 AC: 88772 AN: 151844 Hom.: 27075 Cov.: 31 AF XY: 0.583 AC XY: 43283 AN XY: 74188

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.617

Alfa AF: 0.657 Hom.: 71003

Bravo AF: 0.573

Asia WGS AF: 0.541 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424401; hg19: chr18-53640779;