rs2584316

Variant names:

• chr1-222037987-A-G
• rs2584316
• ENST00000658927.1:n.382-4316T>C

Variant summary

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

The ENST00000658927.1(LINC01705):​n.382-4316T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,000 control chromosomes in the GnomAD database, including 10,310 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 (10310 hom., cov: 32)
• Consequence: LINC01705 ENST00000658927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 2 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=-0.95).
• 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.382-4316T>C		intron_variant	Intron 2 of 2
LINC01705	ENST00000668844.1	n.354+20427T>C		intron_variant	Intron 2 of 2
LINC01705	ENST00000715677.1	n.354+20427T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55059 AN: 151882 Hom.: 10314 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.362 AC: 55065 AN: 152000 Hom.: 10310 Cov.: 32 AF XY: 0.367 AC XY: 27261 AN XY: 74302

African (AFR) AF: 0.281 AC: 11632 AN: 41450

American (AMR) AF: 0.367 AC: 5616 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3472

East Asian (EAS) AF: 0.314 AC: 1624 AN: 5170

South Asian (SAS) AF: 0.344 AC: 1656 AN: 4816

European-Finnish (FIN) AF: 0.491 AC: 5181 AN: 10548

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26627 AN: 67948

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

Alfa AF: 0.383 Hom.: 9287

Bravo AF: 0.349

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.46
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2584316; hg19: chr1-222211329; COSMIC: COSV71538787;