18-24556605-A-G

Variant names:

• chr18-24556605-A-G
• rs12954803
• ENST00000664008.1:n.511+21544A>G

Variant summary

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

The ENST00000664008.1(LINC01915):​n.511+21544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,310 control chromosomes in the GnomAD database, including 1,576 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 0.13 (1576 hom., cov: 33)
• Consequence: LINC01915 ENST00000664008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704
• Publications: 3 publications found

Genes affected

LINC01915 (HGNC:52734): (long intergenic non-protein coding RNA 1915)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664008.1. 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
	LINC01915	ENST00000664008.1		n.511+21544A>G		intron	N/A
	LINC01915	ENST00000762860.1		n.142+21544A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20095 AN: 152192 Hom.: 1575 Cov.: 33

Gnomad AFR AF: 0.0718

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.132 AC: 20109 AN: 152310 Hom.: 1576 Cov.: 33 AF XY: 0.131 AC XY: 9739 AN XY: 74472

African (AFR) AF: 0.0719 AC: 2991 AN: 41572

American (AMR) AF: 0.109 AC: 1666 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3464

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5186

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4824

European-Finnish (FIN) AF: 0.118 AC: 1252 AN: 10614

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11469 AN: 68034

Other (OTH) AF: 0.136 AC: 287 AN: 2110

Alfa AF: 0.0687 Hom.: 101

Bravo AF: 0.124

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.62
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs12954803; hg19: chr18-22136569;