2-85537845-T-G

Variant names:

• chr2-85537845-T-G
• rs1048739
• ENST00000667933.3:n.1266A>C

Variant summary

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

The ENST00000667933.3(PARTICL):​n.1266A>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 ENST00000667933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 5 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=-0.81).
• 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 rank	MANE	Protein	UniProt
PARTICL	NR_038942.1	n.1042A>C		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.1266A>C		non_coding_transcript_exon_variant	Exon 1 of 1
PARTICL	ENST00000737206.1	n.315+658A>C		intron_variant	Intron 1 of 1
PARTICL	ENST00000737207.1	n.311+658A>C		intron_variant	Intron 1 of 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

African (AFR) AF: 0.365 AC: 15108 AN: 41382

American (AMR) AF: 0.227 AC: 3468 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 744 AN: 3466

East Asian (EAS) AF: 0.323 AC: 1664 AN: 5150

South Asian (SAS) AF: 0.169 AC: 811 AN: 4810

European-Finnish (FIN) AF: 0.319 AC: 3369 AN: 10552

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19073 AN: 67840

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.256 Hom.: 1233

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1048739; hg19: chr2-85764968;