rs764377

Variant names:

• chr12-127897105-C-T
• rs764377
• ENST00000614177.2:n.459C>T

Variant summary

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

The ENST00000614177.2(LINC02393):​n.459C>T 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 0.215 in 152,168 control chromosomes in the GnomAD database, including 5,302 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 (5302 hom., cov: 33)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: LINC02393 ENST00000614177.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614177.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02393	NR_033987.1		n.486C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC00508	NR_126452.2		n.312-12000G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02393	ENST00000614177.2	TSL:2	n.459C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC02393	ENST00000662498.1		n.393C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC00508	ENST00000741352.1		n.317-35249G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32639 AN: 152016 Hom.: 5298 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.176 AC: 6 AN: 34 Hom.: 0 Cov.: 0 AF XY: 0.182 AC XY: 4 AN XY: 22

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.143 AC: 4 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.215 AC: 32672 AN: 152134 Hom.: 5302 Cov.: 33 AF XY: 0.214 AC XY: 15904 AN XY: 74376

African (AFR) AF: 0.438 AC: 18178 AN: 41474

American (AMR) AF: 0.138 AC: 2108 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.492 AC: 2537 AN: 5152

South Asian (SAS) AF: 0.0892 AC: 431 AN: 4830

European-Finnish (FIN) AF: 0.138 AC: 1464 AN: 10582

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7223 AN: 68020

Other (OTH) AF: 0.188 AC: 398 AN: 2114

Alfa AF: 0.165 Hom.: 1399

Bravo AF: 0.228

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs764377;

hg19: chr12-128381650;