18-55924136-G-C

Variant names:

• chr18-55924136-G-C
• rs784395
• ENST00000589440.1:n.405+30694G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000589440.1(LINC01905):​n.405+30694G>C variant causes a intron 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: LINC01905 ENST00000589440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 0 publications found

Genes affected

LINC01905 (HGNC:52724): (long intergenic non-protein coding RNA 1905)

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589440.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01905	ENST00000589440.1	TSL:2	n.405+30694G>C		intron	N/A
	LINC01416	ENST00000654280.1		n.1513-25709C>G		intron	N/A
	LINC01416	ENST00000655696.1		n.1304-25709C>G		intron	N/A

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

African (AFR) AF: 0.529 AC: 21915 AN: 41410

American (AMR) AF: 0.542 AC: 8271 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2014 AN: 3468

East Asian (EAS) AF: 0.838 AC: 4324 AN: 5162

South Asian (SAS) AF: 0.772 AC: 3711 AN: 4804

European-Finnish (FIN) AF: 0.658 AC: 6922 AN: 10520

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43459 AN: 67918

Other (OTH) AF: 0.627 AC: 1325 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs784395; hg19: chr18-53591367;