chr2-85538348-G-A

Variant names:

• chr2-85538348-G-A
• rs72940558
• ENST00000667933.3:n.763C>T

Variant summary

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

The ENST00000667933.3(PARTICL):​n.763C>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 0.0292 in 152,256 control chromosomes in the GnomAD database, including 203 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 0.029 (203 hom., cov: 33)
• Consequence: PARTICL ENST00000667933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.17
• Publications: 0 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARTICL	NR_038942.1	n.539C>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.763C>T		non_coding_transcript_exon_variant	Exon 1 of 1
PARTICL	ENST00000737206.1	n.315+155C>T		intron_variant	Intron 1 of 1
PARTICL	ENST00000737207.1	n.311+155C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0291 AC: 4425 AN: 152138 Hom.: 200 Cov.: 33

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00122

Gnomad OTH AF: 0.0224

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

GnomAD4 genome AF: 0.0292 AC: 4452 AN: 152256 Hom.: 203 Cov.: 33 AF XY: 0.0282 AC XY: 2101 AN XY: 74460

African (AFR) AF: 0.0959 AC: 3984 AN: 41530

American (AMR) AF: 0.0148 AC: 227 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.00580 AC: 30 AN: 5176

South Asian (SAS) AF: 0.0104 AC: 50 AN: 4830

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00122 AC: 83 AN: 68014

Other (OTH) AF: 0.0222 AC: 47 AN: 2116

Alfa AF: 0.0256 Hom.: 24

Bravo AF: 0.0326

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs72940558; hg19: chr2-85765471;