rs12759486

Variant names:

• chr1-221893194-C-T
• rs12759486
• ENST00000433576.6:n.483-9306G>A

Variant summary

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

The ENST00000715677.1(LINC01705):​n.634+25398G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,842 control chromosomes in the GnomAD database, including 17,267 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 0.47 (17267 hom., cov: 31)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

Genes affected

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

ENSG00000307440 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715677.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01705	ENST00000433576.6	TSL:5	n.483-9306G>A		intron	N/A
	LINC01705	ENST00000715677.1		n.634+25398G>A		intron	N/A
	LINC01705	ENST00000826165.1		n.476+25398G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70742 AN: 151724 Hom.: 17254 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.466 AC: 70795 AN: 151842 Hom.: 17267 Cov.: 31 AF XY: 0.462 AC XY: 34267 AN XY: 74188

African (AFR) AF: 0.594 AC: 24567 AN: 41386

American (AMR) AF: 0.376 AC: 5745 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1221 AN: 5164

South Asian (SAS) AF: 0.506 AC: 2429 AN: 4804

European-Finnish (FIN) AF: 0.398 AC: 4183 AN: 10522

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29554 AN: 67928

Other (OTH) AF: 0.477 AC: 1002 AN: 2100

Alfa AF: 0.442 Hom.: 3378

Bravo AF: 0.464

Asia WGS AF: 0.386 AC: 1343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.8
DANN	Benign	0.66
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12759486; hg19: chr1-222066536;