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 ENST00000433576.6(LINC01705):​n.483-9306G>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 ENST00000433576.6 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.331-22884C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000433576.6	n.483-9306G>A		intron_variant	Intron 4 of 5	5
LINC01705	ENST00000715677.1	n.634+25398G>A		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.476+25398G>A		intron_variant	Intron 3 of 3

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 v4.3

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;