rs1992045

chr8-57928365-C-T

Variant summary

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

The ENST00000650579.1(LINC01602):n.327-52529C>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 0.133 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375856	XR_928921.2	n.349-29911C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01602	ENST00000650579.1	n.327-52529C>T		intron_variant, non_coding_transcript_variant
	ENST00000664574.1	n.104+5861G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0698

Gnomad4 SAS AF: 0.0869

Gnomad4 FIN AF: 0.0409

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0818 Hom.: 1422

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1992045; hg19: chr8-58840924;