1-83770751-G-C

Variant names:

• chr1-83770751-G-C
• rs10489500
• ENST00000417975.1:n.179-20452C>G

Variant summary

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

The ENST00000417975.1(LINC01725):​n.179-20452C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,046 control chromosomes in the GnomAD database, including 952 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 0.10 (952 hom., cov: 33)
• Consequence: LINC01725 ENST00000417975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

Genes affected

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

ENSG00000237076 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01725	NR_119375.1	n.179-20452C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01725	ENST00000417975.1	n.179-20452C>G		intron_variant	Intron 1 of 2	1
LINC01725	ENST00000670031.2	n.207-20452C>G		intron_variant	Intron 1 of 2
LINC01725	ENST00000685925.1	n.201-20452C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15407 AN: 151928 Hom.: 952 Cov.: 33

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0958

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.101 AC: 15402 AN: 152046 Hom.: 952 Cov.: 33 AF XY: 0.0986 AC XY: 7326 AN XY: 74328

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.0998

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0568 Hom.: 70

Bravo AF: 0.0987

Asia WGS AF: 0.0800 AC: 277 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489500; hg19: chr1-84236434;