2-85538316-C-T

Position:

• chr2-85538316-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARTICL	NR_038942.1	n.571G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARTICL	ENST00000667933.2	n.468G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.173

Alfa AF: 0.0984 Hom.: 212

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4258795; hg19: chr2-85765439;