chr1-69113569-G-A

Variant names:

• chr1-69113569-G-A
• rs4147141
• ENST00000425517.1:n.317+25007G>A

Variant summary

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

The ENST00000425517.1(LINC01707):​n.317+25007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,024 control chromosomes in the GnomAD database, including 23,749 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 0.54 (23749 hom., cov: 32)
• Consequence: LINC01707 ENST00000425517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01707	NR_146608.1	n.317+25007G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01707	ENST00000425517.1	n.317+25007G>A		intron_variant	Intron 3 of 4	3
LINC01707	ENST00000658427.1	n.329+28271G>A		intron_variant	Intron 2 of 3
LINC01707	ENST00000660251.1	n.264+28271G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82411 AN: 151904 Hom.: 23743 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.542 AC: 82430 AN: 152024 Hom.: 23749 Cov.: 32 AF XY: 0.543 AC XY: 40326 AN XY: 74298

African (AFR) AF: 0.338 AC: 13998 AN: 41450

American (AMR) AF: 0.652 AC: 9964 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2220 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2539 AN: 5158

South Asian (SAS) AF: 0.543 AC: 2620 AN: 4822

European-Finnish (FIN) AF: 0.586 AC: 6182 AN: 10544

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42853 AN: 67982

Other (OTH) AF: 0.589 AC: 1243 AN: 2112

Alfa AF: 0.598 Hom.: 42025

Bravo AF: 0.535

Asia WGS AF: 0.486 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.81
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs4147141; hg19: chr1-69579252;