ENST00000667933.3:n.1029G>T

Variant names:

• chr2-85538082-C-A
• rs6729475
• ENST00000667933.3:n.1029G>T

Variant summary

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

The ENST00000667933.3(PARTICL):​n.1029G>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 0.16 in 152,196 control chromosomes in the GnomAD database, including 2,483 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 0.16 (2483 hom., cov: 32)
• Consequence: PARTICL ENST00000667933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 7 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARTICL	NR_038942.1	n.805G>T		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARTICL	ENST00000667933.3	n.1029G>T		non_coding_transcript_exon_variant	Exon 1 of 1
PARTICL	ENST00000737206.1	n.315+421G>T		intron_variant	Intron 1 of 1
PARTICL	ENST00000737207.1	n.311+421G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24372 AN: 152080 Hom.: 2482 Cov.: 32

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.160 AC: 24379 AN: 152196 Hom.: 2483 Cov.: 32 AF XY: 0.158 AC XY: 11785 AN XY: 74406

African (AFR) AF: 0.0535 AC: 2224 AN: 41552

American (AMR) AF: 0.146 AC: 2238 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 581 AN: 3472

East Asian (EAS) AF: 0.0187 AC: 97 AN: 5184

South Asian (SAS) AF: 0.0734 AC: 354 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2626 AN: 10588

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15573 AN: 67978

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.207 Hom.: 2243

Bravo AF: 0.149

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6729475; hg19: chr2-85765205; COSMIC: COSV60573401;