chr18-55983078-A-G

Variant names:

• chr18-55983078-A-G
• rs2902193
• ENST00000589440.1:n.406-34650A>G

Variant summary

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

The ENST00000589440.1(LINC01905):​n.406-34650A>G variant causes a intron 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: LINC01905 ENST00000589440.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 2 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=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01905	ENST00000589440.1	n.406-34650A>G		intron_variant	Intron 1 of 2	2
LINC01416	ENST00000654280.1	n.1512+13630T>C		intron_variant	Intron 1 of 3
LINC01416	ENST00000655696.1	n.1303+13630T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.410 AC: 17009 AN: 41450

American (AMR) AF: 0.576 AC: 8791 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3470

East Asian (EAS) AF: 0.472 AC: 2425 AN: 5134

South Asian (SAS) AF: 0.605 AC: 2908 AN: 4810

European-Finnish (FIN) AF: 0.551 AC: 5819 AN: 10560

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37733 AN: 67944

Other (OTH) AF: 0.538 AC: 1135 AN: 2110

Alfa AF: 0.539 Hom.: 67535

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2902193; hg19: chr18-53650309;