rs16973225

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01418	XR_001751639.2	n.402-11633T>G		intron_variant	Intron 3 of 6
LINC01418	XR_001751640.2	n.414-11633T>G		intron_variant	Intron 3 of 5
LINC01418	XR_001751641.2	n.116-7533T>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01418	ENST00000559299.2	n.527-11633T>G		intron_variant	Intron 3 of 7	4
LINC01418	ENST00000657769.1	n.1182-11633T>G		intron_variant	Intron 6 of 8
LINC01418	ENST00000829414.1	n.757-11633T>G		intron_variant	Intron 5 of 7

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 v4.3

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;