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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375856	XR_928921.2	n.349-29911C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01602	ENST00000650579.1	n.327-52529C>T		intron_variant	Intron 2 of 3
ENSG00000253376	ENST00000664574.1	n.104+5861G>A		intron_variant	Intron 1 of 2
LINC01602	ENST00000805089.1	n.375-29911C>T		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs1992045; hg19: chr8-58840924;