chr12-52193734-G-T

Variant names:

• chr12-52193734-G-T
• rs17653722
• ENST00000640420.2:n.413+28783G>T

Variant summary

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

The ENST00000640420.2(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 ENST00000640420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.718
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000640420.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00592	ENST00000640420.2	TSL:5	n.413+28783G>T		intron	N/A
	LINC00592	ENST00000806698.1		n.442+6086G>T		intron	N/A
	LINC00592	ENST00000806699.1		n.438+6086G>T		intron	N/A

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

African (AFR) AF: 0.0532 AC: 2212 AN: 41588

American (AMR) AF: 0.122 AC: 1861 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3470

East Asian (EAS) AF: 0.126 AC: 651 AN: 5182

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4828

European-Finnish (FIN) AF: 0.0928 AC: 985 AN: 10614

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11300 AN: 68018

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.157 Hom.: 1931

Bravo AF: 0.125

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.45
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs17653722; hg19: chr12-52587518;