rs7539409

Positions:

• chr1-83789052-G-A
• chr1-83789052-G-C
• chr1-83789052-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_119375.1(LINC01725):​n.179-38753C>T variant causes a intron, non coding transcript 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 NR_119375.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01725	NR_119375.1	n.179-38753C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01725	ENST00000417975.1	n.179-38753C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000701697.1	n.310-11642G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.875

Alfa AF: 0.869 Hom.: 124675

Bravo AF: 0.906

Asia WGS AF: 0.870 AC: 3025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7539409; hg19: chr1-84254735;