ENST00000415532.3:n.175-34250G>A

Variant names:

• chr1-101689492-G-A
• rs6703780
• ENST00000415532.3:n.175-34250G>A

Variant summary

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

The ENST00000415532.3(LINC01709):​n.175-34250G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,136 control chromosomes in the GnomAD database, including 5,714 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 0.16 (5714 hom., cov: 32)
• Consequence: LINC01709 ENST00000415532.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 0 publications found

Genes affected

LINC01709 (HGNC:52497): (long intergenic non-protein coding RNA 1709)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01709	NR_183470.1	n.297-34250G>A		intron_variant	Intron 3 of 4
LINC01709	NR_183471.1	n.230-34250G>A		intron_variant	Intron 2 of 3
LINC01709	NR_183472.1	n.131-34250G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01709	ENST00000415532.3	n.175-34250G>A		intron_variant	Intron 1 of 2	5
LINC01709	ENST00000635702.1	n.218-34250G>A		intron_variant	Intron 2 of 6	5
LINC01709	ENST00000648951.1	n.157-34250G>A		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24717 AN: 152020 Hom.: 5675 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0928

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0170

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.163 AC: 24821 AN: 152136 Hom.: 5714 Cov.: 32 AF XY: 0.159 AC XY: 11808 AN XY: 74380

African (AFR) AF: 0.517 AC: 21448 AN: 41466

American (AMR) AF: 0.0742 AC: 1132 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3466

East Asian (EAS) AF: 0.0177 AC: 92 AN: 5188

South Asian (SAS) AF: 0.0925 AC: 446 AN: 4824

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10596

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0170 AC: 1158 AN: 68012

Other (OTH) AF: 0.134 AC: 283 AN: 2112

Alfa AF: 0.0283 Hom.: 101

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.61
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs6703780; hg19: chr1-102155048;