rs17653722

Positions:

• chr12-52193734-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00592	ENST00000640420.1	n.413+28783G>T		intron_variant, non_coding_transcript_variant		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;