ENST00000667933.3:n.1268T>A

Variant names:

• chr2-85537843-A-T
• rs1048740
• ENST00000667933.3:n.1268T>A

Variant summary

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

The ENST00000667933.3(PARTICL):​n.1268T>A 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 0.298 in 151,782 control chromosomes in the GnomAD database, including 6,942 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 0.30 (6942 hom., cov: 32)
• Consequence: PARTICL ENST00000667933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 5 publications found

Genes affected

PARTICL (HGNC:50886): (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667933.3. 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
	PARTICL	NR_038942.1		n.1044T>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARTICL	ENST00000667933.3		n.1268T>A		non_coding_transcript_exon	Exon 1 of 1
	PARTICL	ENST00000737206.1		n.315+660T>A		intron	N/A
	PARTICL	ENST00000737207.1		n.311+660T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45187 AN: 151664 Hom.: 6930 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.298 AC: 45226 AN: 151782 Hom.: 6942 Cov.: 32 AF XY: 0.296 AC XY: 21949 AN XY: 74178

African (AFR) AF: 0.365 AC: 15104 AN: 41388

American (AMR) AF: 0.227 AC: 3467 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5152

South Asian (SAS) AF: 0.168 AC: 809 AN: 4802

European-Finnish (FIN) AF: 0.319 AC: 3369 AN: 10548

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.281 AC: 19076 AN: 67866

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.270 Hom.: 755

Bravo AF: 0.299

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.91
DANN	Benign	0.76
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1048740; hg19: chr2-85764966;