rs1992045

Variant names:

• chr8-57928365-C-T
• rs1992045
• ENST00000650579.1:n.327-52529C>T

Variant summary

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

The ENST00000650579.1(LINC01602):​n.327-52529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,200 control chromosomes in the GnomAD database, including 1,899 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 0.13 (1899 hom., cov: 32)
• Consequence: LINC01602 ENST00000650579.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 13 publications found

Genes affected

LINC01602 (HGNC:51634): (long intergenic non-protein coding RNA 1602)

ENSG00000253376 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650579.1. 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
	LINC01602	ENST00000650579.1		n.327-52529C>T		intron	N/A
	ENSG00000253376	ENST00000664574.1		n.104+5861G>A		intron	N/A
	LINC01602	ENST00000805089.1		n.375-29911C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20126 AN: 152082 Hom.: 1891 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.0409

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.133 AC: 20174 AN: 152200 Hom.: 1899 Cov.: 32 AF XY: 0.132 AC XY: 9811 AN XY: 74404

African (AFR) AF: 0.274 AC: 11355 AN: 41494

American (AMR) AF: 0.129 AC: 1966 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3468

East Asian (EAS) AF: 0.0698 AC: 361 AN: 5172

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4824

European-Finnish (FIN) AF: 0.0409 AC: 434 AN: 10618

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0718 AC: 4887 AN: 68024

Other (OTH) AF: 0.132 AC: 278 AN: 2112

Alfa AF: 0.0903 Hom.: 3979

Bravo AF: 0.143

Asia WGS AF: 0.0940 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.39
PhyloP100		-0.84

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1992045;

hg19: chr8-58840924;