rs2902193

chr18-55983078-A-Gchr18-55983078-A-T

Variant summary

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

The ENST00000589440.1(LINC03092):n.406-34650A>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 0.517 in 151,940 control chromosomes in the GnomAD database, including 20,804 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 0.52 (20804 hom., cov: 31)
• Consequence: LINC03092 ENST00000589440.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 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.406-34650A>G		intron_variant, non_coding_transcript_variant		2
LINC01416	ENST00000654280.1	n.1512+13630T>C		intron_variant, non_coding_transcript_variant
LINC01416	ENST00000655696.1	n.1303+13630T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78519 AN: 151822 Hom.: 20761 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.517 AC: 78627 AN: 151940 Hom.: 20804 Cov.: 31 AF XY: 0.521 AC XY: 38658 AN XY: 74214

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.538

Alfa AF: 0.546 Hom.: 43874

Bravo AF: 0.507

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.3
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2902193; hg19: chr18-53650309;