rs1446668

Variant names:

• chr2-85537837-G-T
• rs1446668
• ENST00000667933.3:n.1274C>A

Variant summary

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

The ENST00000667933.3(PARTICL):​n.1274C>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 0.536 in 151,718 control chromosomes in the GnomAD database, including 23,352 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 0.54 (23352 hom., cov: 31)
• Consequence: PARTICL ENST00000667933.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 26 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARTICL	NR_038942.1	n.1050C>A		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.1274C>A		non_coding_transcript_exon_variant	Exon 1 of 1
PARTICL	ENST00000737206.1	n.315+666C>A		intron_variant	Intron 1 of 1
PARTICL	ENST00000737207.1	n.311+666C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81277 AN: 151600 Hom.: 23322 Cov.: 31

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.536 AC: 81357 AN: 151718 Hom.: 23352 Cov.: 31 AF XY: 0.532 AC XY: 39488 AN XY: 74186

African (AFR) AF: 0.759 AC: 31380 AN: 41368

American (AMR) AF: 0.435 AC: 6630 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2002 AN: 5152

South Asian (SAS) AF: 0.395 AC: 1897 AN: 4806

European-Finnish (FIN) AF: 0.457 AC: 4819 AN: 10538

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31608 AN: 67844

Other (OTH) AF: 0.520 AC: 1097 AN: 2108

Alfa AF: 0.524 Hom.: 11731

Bravo AF: 0.544

Asia WGS AF: 0.443 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.66
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1446668; hg19: chr2-85764960;