1-69193736-A-G

Variant names:

• chr1-69193736-A-G
• rs10493453
• ENST00000658427.1:n.330-24628A>G

Variant summary

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

The ENST00000658427.1(LINC01707):​n.330-24628A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,864 control chromosomes in the GnomAD database, including 1,690 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 0.15 (1690 hom., cov: 31)
• Consequence: LINC01707 ENST00000658427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 2 publications found

Genes affected

LINC01707 (HGNC:52495): (long intergenic non-protein coding RNA 1707)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658427.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01707	ENST00000658427.1		n.330-24628A>G		intron	N/A
	LINC01707	ENST00000660251.1		n.552+1150A>G		intron	N/A
	LINC01707	ENST00000661832.1		n.481+1150A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22657 AN: 151748 Hom.: 1688 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.149 AC: 22689 AN: 151864 Hom.: 1690 Cov.: 31 AF XY: 0.153 AC XY: 11350 AN XY: 74250

African (AFR) AF: 0.163 AC: 6752 AN: 41424

American (AMR) AF: 0.136 AC: 2070 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3466

East Asian (EAS) AF: 0.193 AC: 987 AN: 5124

South Asian (SAS) AF: 0.163 AC: 787 AN: 4820

European-Finnish (FIN) AF: 0.204 AC: 2145 AN: 10496

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

European-Non Finnish (NFE) AF: 0.135 AC: 9150 AN: 67954

Other (OTH) AF: 0.139 AC: 294 AN: 2114

Alfa AF: 0.143 Hom.: 222

Bravo AF: 0.148

Asia WGS AF: 0.180 AC: 622 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.78
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10493453; hg19: chr1-69659419;