ENST00000715677.1:n.355-10513G>T

Variant names:

• chr1-221989031-C-A
• rs6691195
• ENST00000715677.1:n.355-10513G>T

Variant summary

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

The ENST00000715677.1(LINC01705):​n.355-10513G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,132 control chromosomes in the GnomAD database, including 2,947 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 0.19 (2947 hom., cov: 32)
• Consequence: LINC01705 ENST00000715677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 11 publications found

Genes affected

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

ENSG00000307458 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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	ENST00000715677.1	n.355-10513G>T		intron_variant	Intron 2 of 4
LINC01705	ENST00000826165.1	n.355+69383G>T		intron_variant	Intron 2 of 3
LINC01705	ENST00000826166.1	n.265+69383G>T		intron_variant	Intron 1 of 2
ENSG00000307458	ENST00000826417.1	n.97+12313C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28939 AN: 152014 Hom.: 2948 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.190 AC: 28935 AN: 152132 Hom.: 2947 Cov.: 32 AF XY: 0.194 AC XY: 14397 AN XY: 74388

African (AFR) AF: 0.147 AC: 6100 AN: 41502

American (AMR) AF: 0.228 AC: 3487 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 633 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1124 AN: 5176

South Asian (SAS) AF: 0.155 AC: 746 AN: 4810

European-Finnish (FIN) AF: 0.267 AC: 2820 AN: 10572

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13405 AN: 67990

Other (OTH) AF: 0.188 AC: 397 AN: 2108

Alfa AF: 0.196 Hom.: 1923

Bravo AF: 0.186

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.14
DANN	Benign	0.67
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6691195; hg19: chr1-222162373; COSMIC: COSV71499210;