ENST00000715677.1:n.635-18690G>A

Variant names:

• chr1-221859143-C-T
• rs12144971
• ENST00000715677.1:n.635-18690G>A

Variant summary

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

The ENST00000715677.1(LINC01705):​n.635-18690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,072 control chromosomes in the GnomAD database, including 22,083 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 0.53 (22083 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.330+7078C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000715677.1	n.635-18690G>A		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.477-18690G>A		intron_variant	Intron 3 of 3
LINC01705	ENST00000826167.1	n.470-18690G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81116 AN: 151954 Hom.: 22060 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.534 AC: 81191 AN: 152072 Hom.: 22083 Cov.: 32 AF XY: 0.531 AC XY: 39451 AN XY: 74322

African (AFR) AF: 0.499 AC: 20700 AN: 41446

American (AMR) AF: 0.427 AC: 6525 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1690 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5168

South Asian (SAS) AF: 0.538 AC: 2590 AN: 4818

European-Finnish (FIN) AF: 0.571 AC: 6030 AN: 10568

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39758 AN: 67990

Other (OTH) AF: 0.527 AC: 1111 AN: 2110

Alfa AF: 0.562 Hom.: 92307

Bravo AF: 0.517

Asia WGS AF: 0.430 AC: 1499 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	2.9
DANN	Benign	0.56
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12144971; hg19: chr1-222032485; COSMIC: COSV60032674;