2-85537845-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038942.1(PARTICL):n.1042A>C 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 0.298 in 151,760 control chromosomes in the GnomAD database, including 6,938 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 0.30 (6938 hom., cov: 32)
• Consequence: PARTICL NR_038942.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARTICL	NR_038942.1	n.1042A>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARTICL	ENST00000667933.2	n.939A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45184 AN: 151642 Hom.: 6926 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.298 AC: 45223 AN: 151760 Hom.: 6938 Cov.: 32 AF XY: 0.296 AC XY: 21953 AN XY: 74194

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.287

Alfa AF: 0.152 Hom.: 304

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.90
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1048739; hg19: chr2-85764968;