ENST00000715677.1:n.635-24577C>T

Variant names:

• chr1-221865030-G-A
• rs12130910
• ENST00000715677.1:n.635-24577C>T

Variant summary

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

The ENST00000715677.1(LINC01705):​n.635-24577C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,026 control chromosomes in the GnomAD database, including 8,199 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 0.32 (8199 hom., cov: 33)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904517	XR_007066885.1	n.330+12965G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01705	ENST00000715677.1	n.635-24577C>T		intron_variant	Intron 4 of 4
LINC01705	ENST00000826165.1	n.477-24577C>T		intron_variant	Intron 3 of 3
LINC01705	ENST00000826167.1	n.470-24577C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48622 AN: 151910 Hom.: 8199 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.320 AC: 48651 AN: 152026 Hom.: 8199 Cov.: 33 AF XY: 0.316 AC XY: 23488 AN XY: 74306

African (AFR) AF: 0.339 AC: 14039 AN: 41466

American (AMR) AF: 0.245 AC: 3737 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3472

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5180

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3811 AN: 10534

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23354 AN: 67956

Other (OTH) AF: 0.325 AC: 688 AN: 2114

Alfa AF: 0.333 Hom.: 4693

Bravo AF: 0.308

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.22
DANN	Benign	0.69
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12130910; hg19: chr1-222038372; COSMIC: COSV60032690;