2-85535086-T-C

Variant names:

• chr2-85535086-T-C
• rs1446669
• ENST00000737206.1:n.324A>G

Variant summary

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

The ENST00000737206.1(PARTICL):​n.324A>G 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 0.318 in 152,004 control chromosomes in the GnomAD database, including 7,854 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 0.32 (7854 hom., cov: 31)
• Consequence: PARTICL ENST00000737206.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528
• Publications: 22 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARTICL	ENST00000737206.1	n.324A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48306 AN: 151886 Hom.: 7843 Cov.: 31

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.318 AC: 48347 AN: 152004 Hom.: 7854 Cov.: 31 AF XY: 0.316 AC XY: 23512 AN XY: 74304

African (AFR) AF: 0.372 AC: 15396 AN: 41438

American (AMR) AF: 0.258 AC: 3944 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1710 AN: 5174

South Asian (SAS) AF: 0.196 AC: 945 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3805 AN: 10546

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20679 AN: 67972

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.307 Hom.: 22914

Bravo AF: 0.315

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	16
DANN	Benign	0.77
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1446669; hg19: chr2-85762209;