rs784395

chr18-55924136-G-Cchr18-55924136-G-T

Variant summary

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

The ENST00000589440.1(LINC03092):n.405+30694G>C 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 0.61 in 151,848 control chromosomes in the GnomAD database, including 28,653 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 0.61 (28653 hom., cov: 31)
• Consequence: LINC03092 ENST00000589440.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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 (EAS) allele frequency at 95% confidence interval = 0.817 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.405+30694G>C		intron_variant, non_coding_transcript_variant		2
LINC01416	ENST00000654280.1	n.1513-25709C>G		intron_variant, non_coding_transcript_variant
LINC01416	ENST00000655696.1	n.1304-25709C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92547 AN: 151730 Hom.: 28634 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.610 AC: 92608 AN: 151848 Hom.: 28653 Cov.: 31 AF XY: 0.614 AC XY: 45540 AN XY: 74194

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.627

Alfa AF: 0.541 Hom.: 1747

Bravo AF: 0.598

Asia WGS AF: 0.740 AC: 2571 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	0.24
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs784395; hg19: chr18-53591367;