15-81937658-A-C

Variant names:

• chr15-81937658-A-C
• rs16973225
• ENST00000559299.2:n.527-11633T>G

Variant summary

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

The ENST00000559299.2(LINC01418):​n.527-11633T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 152,210 control chromosomes in the GnomAD database, including 730 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 0.078 (730 hom., cov: 33)
• Consequence: LINC01418 ENST00000559299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 15 publications found

Genes affected

LINC01418 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559299.2. 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
	LINC01418	ENST00000559299.2	TSL:4	n.527-11633T>G		intron	N/A
	LINC01418	ENST00000657769.1		n.1182-11633T>G		intron	N/A
	LINC01418	ENST00000829414.1		n.757-11633T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 11927 AN: 152090 Hom.: 727 Cov.: 33

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0785 AC: 11943 AN: 152210 Hom.: 730 Cov.: 33 AF XY: 0.0855 AC XY: 6365 AN XY: 74426

African (AFR) AF: 0.0852 AC: 3539 AN: 41514

American (AMR) AF: 0.125 AC: 1907 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0216 AC: 75 AN: 3472

East Asian (EAS) AF: 0.166 AC: 863 AN: 5184

South Asian (SAS) AF: 0.329 AC: 1589 AN: 4826

European-Finnish (FIN) AF: 0.0586 AC: 621 AN: 10602

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3175 AN: 68022

Other (OTH) AF: 0.0734 AC: 155 AN: 2112

Alfa AF: 0.0576 Hom.: 1293

Bravo AF: 0.0797

Asia WGS AF: 0.251 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.64
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs16973225; hg19: chr15-82229999;