2-85536883-C-T

Variant names:

• chr2-85536883-C-T
• rs3755014
• ENST00000737207.1:n.434G>A

Variant summary

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

The ENST00000737207.1(PARTICL):​n.434G>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 0.531 in 152,042 control chromosomes in the GnomAD database, including 22,835 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 0.53 (22835 hom., cov: 32)
• Consequence: PARTICL ENST00000737207.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 16 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARTICL	ENST00000737207.1	n.434G>A		non_coding_transcript_exon_variant	Exon 2 of 2
PARTICL	ENST00000737206.1	n.315+1620G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80618 AN: 151924 Hom.: 22800 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.531 AC: 80708 AN: 152042 Hom.: 22835 Cov.: 32 AF XY: 0.527 AC XY: 39140 AN XY: 74308

African (AFR) AF: 0.737 AC: 30596 AN: 41496

American (AMR) AF: 0.431 AC: 6587 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3470

East Asian (EAS) AF: 0.392 AC: 2021 AN: 5156

South Asian (SAS) AF: 0.396 AC: 1910 AN: 4824

European-Finnish (FIN) AF: 0.458 AC: 4823 AN: 10542

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.467 AC: 31740 AN: 67974

Other (OTH) AF: 0.521 AC: 1098 AN: 2106

Alfa AF: 0.480 Hom.: 7785

Bravo AF: 0.536

Asia WGS AF: 0.441 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.21
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3755014; hg19: chr2-85764006;