18-24556605-A-G

Position:

• chr18-24556605-A-G

Variant summary

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

The ENST00000664008.1(LINC01915):​n.511+21544A>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 0.132 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.704

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01915	ENST00000664008.1	n.511+21544A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0719

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0131

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0683 Hom.: 98

Bravo AF: 0.124

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12954803; hg19: chr18-22136569;