rs1358652

Variant names:

• chr12-127896889-A-G
• rs1358652
• ENST00000614177.2:n.243A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000614177.2(LINC02393):​n.243A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,196 control chromosomes in the GnomAD database, including 4,985 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 0.21 (4985 hom., cov: 33)
  • Exomes 𝑓: 0.22 (0 hom.)
• Consequence: LINC02393 ENST00000614177.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 3 publications found

Genes affected

LINC02393 (HGNC:53320): (long intergenic non-protein coding RNA 2393)

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02393	NR_033987.1	n.270A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00508	NR_126452.2	n.312-11784T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02393	ENST00000614177.2	n.243A>G		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC02393	ENST00000662498.1	n.177A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00508	ENST00000741352.1	n.317-35033T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31858 AN: 152060 Hom.: 4979 Cov.: 33

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.189

GnomAD4 exome AF: 0.222 AC: 4 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.222 AC XY: 4 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.188 AC: 3 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.210 AC: 31891 AN: 152178 Hom.: 4985 Cov.: 33 AF XY: 0.209 AC XY: 15527 AN XY: 74418

African (AFR) AF: 0.420 AC: 17421 AN: 41484

American (AMR) AF: 0.137 AC: 2097 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2537 AN: 5160

South Asian (SAS) AF: 0.0890 AC: 429 AN: 4822

European-Finnish (FIN) AF: 0.138 AC: 1467 AN: 10608

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7214 AN: 68010

Other (OTH) AF: 0.186 AC: 394 AN: 2116

Alfa AF: 0.161 Hom.: 495

Bravo AF: 0.222

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1358652; hg19: chr12-128381434;