chr1-83789052-G-A

Variant names:

• chr1-83789052-G-A
• rs7539409
• ENST00000417975.1:n.179-38753C>T

Variant summary

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

The ENST00000417975.1(LINC01725):​n.179-38753C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,256 control chromosomes in the GnomAD database, including 61,774 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 0.90 (61774 hom., cov: 32)
• Consequence: LINC01725 ENST00000417975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467
• Publications: 11 publications found

Genes affected

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

ENSG00000237076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417975.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01725	NR_119375.1		n.179-38753C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01725	ENST00000417975.1	TSL:1	n.179-38753C>T		intron	N/A
	LINC01725	ENST00000670031.2		n.207-38753C>T		intron	N/A
	LINC01725	ENST00000685925.2		n.236-38753C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136776 AN: 152138 Hom.: 61722 Cov.: 32

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.899 AC: 136878 AN: 152256 Hom.: 61774 Cov.: 32 AF XY: 0.897 AC XY: 66775 AN XY: 74430

African (AFR) AF: 0.975 AC: 40531 AN: 41566

American (AMR) AF: 0.904 AC: 13839 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2991 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4901 AN: 5186

South Asian (SAS) AF: 0.860 AC: 4150 AN: 4828

European-Finnish (FIN) AF: 0.839 AC: 8885 AN: 10584

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58817 AN: 67996

Other (OTH) AF: 0.875 AC: 1851 AN: 2116

Alfa AF: 0.877 Hom.: 192792

Bravo AF: 0.906

Asia WGS AF: 0.870 AC: 3025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.63
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs7539409; hg19: chr1-84254735;