2-85538318-T-G

Variant names:

• chr2-85538318-T-G
• rs1446667
• ENST00000667933.3:n.793A>C

Variant summary

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

The ENST00000667933.3(PARTICL):​n.793A>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 0.299 in 151,210 control chromosomes in the GnomAD database, including 6,952 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 (6952 hom., cov: 31)
• Consequence: PARTICL ENST00000667933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667933.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARTICL	NR_038942.1		n.569A>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARTICL	ENST00000667933.3		n.793A>C		non_coding_transcript_exon	Exon 1 of 1
	PARTICL	ENST00000737206.1		n.315+185A>C		intron	N/A
	PARTICL	ENST00000737207.1		n.311+185A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45123 AN: 151090 Hom.: 6941 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.299 AC: 45160 AN: 151210 Hom.: 6952 Cov.: 31 AF XY: 0.297 AC XY: 21919 AN XY: 73882

African (AFR) AF: 0.366 AC: 15093 AN: 41198

American (AMR) AF: 0.225 AC: 3423 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 746 AN: 3454

East Asian (EAS) AF: 0.325 AC: 1662 AN: 5106

South Asian (SAS) AF: 0.172 AC: 817 AN: 4750

European-Finnish (FIN) AF: 0.322 AC: 3354 AN: 10420

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19078 AN: 67770

Other (OTH) AF: 0.283 AC: 597 AN: 2106

Alfa AF: 0.309 Hom.: 1739

Bravo AF: 0.298

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.1
DANN	Benign	0.35
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1446667; hg19: chr2-85765441;