rs17653722

Variant names:

• chr12-52193734-G-T
• rs17653722
• ENST00000640420.1:n.413+28783G>T

Variant summary

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

The ENST00000640420.1(LINC00592):​n.413+28783G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,326 control chromosomes in the GnomAD database, including 1,467 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 (1467 hom., cov: 33)
• Consequence: LINC00592 ENST00000640420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718

Genes affected

LINC00592 (HGNC:27474): (long intergenic non-protein coding RNA 592)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00592	ENST00000640420.1	n.413+28783G>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19422 AN: 152208 Hom.: 1468 Cov.: 33

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0928

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.127 AC: 19412 AN: 152326 Hom.: 1467 Cov.: 33 AF XY: 0.128 AC XY: 9509 AN XY: 74476

Gnomad4 AFR AF: 0.0532

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.0928

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.161

Alfa AF: 0.161 Hom.: 1343

Bravo AF: 0.125

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17653722; hg19: chr12-52587518;