rs17023457

Variant names:

• chr1-119333107-T-C
• rs17023457
• ENST00000457683.1:n.82+4318T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000457683.1(LINC01780):​n.82+4318T>C variant causes a intron change. The variant allele was found at a frequency of 0.155 in 152,208 control chromosomes in the GnomAD database, including 2,580 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 0.15 (2580 hom., cov: 33)
• Consequence: LINC01780 ENST00000457683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.90
• Publications: 13 publications found

Genes affected

LINC01780 (HGNC:52570): (long intergenic non-protein coding RNA 1780)

WARS2-AS1 (HGNC:40612): (WARS2 antisense RNA 1)

ENSG00000227712 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457683.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01780	NR_146623.1		n.82+4318T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01780	ENST00000457683.1	TSL:3	n.82+4318T>C		intron	N/A
	WARS2-AS1	ENST00000715919.1		n.727-21310T>C		intron	N/A
	ENSG00000227712	ENST00000840373.1		n.763-145A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23533 AN: 152090 Hom.: 2581 Cov.: 33

Gnomad AFR AF: 0.0369

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23530 AN: 152208 Hom.: 2580 Cov.: 33 AF XY: 0.159 AC XY: 11828 AN XY: 74448

African (AFR) AF: 0.0368 AC: 1529 AN: 41548

American (AMR) AF: 0.293 AC: 4483 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 501 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2199 AN: 5180

South Asian (SAS) AF: 0.136 AC: 656 AN: 4828

European-Finnish (FIN) AF: 0.210 AC: 2223 AN: 10598

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11463 AN: 67990

Other (OTH) AF: 0.151 AC: 318 AN: 2112

Alfa AF: 0.170 Hom.: 5049

Bravo AF: 0.164

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	20
DANN	Benign	0.81
PhyloP100		4.9

Splicing

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

Other links and lift over

dbSNP: rs17023457; hg19: chr1-119875730;