rs2584315

Variant names:

• chr1-222033545-G-A
• rs2584315
• ENST00000658927.1:n.508C>T

Variant summary

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

The ENST00000658927.1(LINC01705):​n.508C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,028 control chromosomes in the GnomAD database, including 10,297 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 0.36 (10297 hom., cov: 32)
• Consequence: LINC01705 ENST00000658927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807
• Publications: 3 publications found

Genes affected

LINC01705 (HGNC:52493): (long intergenic non-protein coding RNA 1705)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 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
LINC01705	ENST00000658927.1	n.508C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01705	ENST00000668844.1	n.355-22202C>T		intron_variant	Intron 2 of 2
LINC01705	ENST00000715677.1	n.354+24869C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55027 AN: 151908 Hom.: 10301 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.362 AC: 55031 AN: 152028 Hom.: 10297 Cov.: 32 AF XY: 0.367 AC XY: 27244 AN XY: 74306

African (AFR) AF: 0.280 AC: 11614 AN: 41466

American (AMR) AF: 0.367 AC: 5613 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1616 AN: 5172

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4820

European-Finnish (FIN) AF: 0.492 AC: 5194 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26607 AN: 67940

Other (OTH) AF: 0.374 AC: 789 AN: 2112

Alfa AF: 0.380 Hom.: 47443

Bravo AF: 0.349

Asia WGS AF: 0.333 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.84
DANN	Benign	0.86
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2584315; hg19: chr1-222206887; COSMIC: COSV107160452;