1-234513073-A-C

Variant names:

• chr1-234513073-A-C
• rs6586395
• ENST00000804324.1:n.262-10517T>G

Variant summary

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

The ENST00000804324.1(LINC01354):​n.262-10517T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,822 control chromosomes in the GnomAD database, including 10,879 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 0.25 (10879 hom., cov: 30)
• Consequence: LINC01354 ENST00000804324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 4 publications found

Genes affected

LINC01354 (HGNC:50581): (long intergenic non-protein coding RNA 1354)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01354	ENST00000804324.1	n.262-10517T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38274 AN: 151704 Hom.: 10829 Cov.: 30

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.00716

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.253 AC: 38380 AN: 151822 Hom.: 10879 Cov.: 30 AF XY: 0.245 AC XY: 18210 AN XY: 74248

African (AFR) AF: 0.704 AC: 29077 AN: 41274

American (AMR) AF: 0.149 AC: 2279 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3470

East Asian (EAS) AF: 0.00737 AC: 38 AN: 5158

South Asian (SAS) AF: 0.0775 AC: 373 AN: 4812

European-Finnish (FIN) AF: 0.0385 AC: 408 AN: 10584

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0795 AC: 5401 AN: 67932

Other (OTH) AF: 0.206 AC: 435 AN: 2110

Alfa AF: 0.164 Hom.: 10450

Bravo AF: 0.282

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.34
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6586395; hg19: chr1-234648819;