2-85538316-C-T

Variant names:

• chr2-85538316-C-T
• rs4258795
• ENST00000667933.3:n.795G>A

Variant summary

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

The NR_038942.1(PARTICL):​n.571G>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 0.159 in 151,988 control chromosomes in the GnomAD database, including 2,432 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 (2432 hom., cov: 32)
• Consequence: PARTICL NR_038942.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• 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 = 0.225 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_038942.1. 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
	PARTICL	NR_038942.1		n.571G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARTICL	ENST00000667933.3		n.795G>A		non_coding_transcript_exon	Exon 1 of 1
	PARTICL	ENST00000737206.1		n.315+187G>A		intron	N/A
	PARTICL	ENST00000737207.1		n.311+187G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24202 AN: 151870 Hom.: 2431 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0188

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.159 AC: 24209 AN: 151988 Hom.: 2432 Cov.: 32 AF XY: 0.157 AC XY: 11692 AN XY: 74280

African (AFR) AF: 0.0531 AC: 2206 AN: 41514

American (AMR) AF: 0.143 AC: 2185 AN: 15284

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

East Asian (EAS) AF: 0.0189 AC: 97 AN: 5136

South Asian (SAS) AF: 0.0737 AC: 355 AN: 4820

European-Finnish (FIN) AF: 0.246 AC: 2591 AN: 10524

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15508 AN: 67922

Other (OTH) AF: 0.173 AC: 364 AN: 2110

Alfa AF: 0.0971 Hom.: 214

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	2.4
DANN	Benign	0.75
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4258795; hg19: chr2-85765439;