rs2584315

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.374

Alfa AF: 0.385 Hom.: 23126

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2584315; hg19: chr1-222206887;