rs72844458

Variant names:

• chr2-85536904-G-C
• rs72844458
• ENST00000737207.1:n.413C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000737207.1(PARTICL):​n.413C>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 0.0357 in 152,288 control chromosomes in the GnomAD database, including 139 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 0.036 (139 hom., cov: 33)
• Consequence: PARTICL ENST00000737207.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649
• Publications: 1 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=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0357 (5435/152288) while in subpopulation NFE AF = 0.0459 (3120/68026). AF 95% confidence interval is 0.0445. There are 139 homozygotes in GnomAd4. There are 2861 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 139 gene

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	ENST00000737207.1	n.413C>G		non_coding_transcript_exon_variant	Exon 2 of 2
PARTICL	ENST00000737206.1	n.315+1599C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5434 AN: 152170 Hom.: 138 Cov.: 33

Gnomad AFR AF: 0.00859

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00931

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0378

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

GnomAD4 genome AF: 0.0357 AC: 5435 AN: 152288 Hom.: 139 Cov.: 33 AF XY: 0.0384 AC XY: 2861 AN XY: 74456

African (AFR) AF: 0.00856 AC: 356 AN: 41570

American (AMR) AF: 0.0367 AC: 561 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00932 AC: 45 AN: 4830

European-Finnish (FIN) AF: 0.105 AC: 1114 AN: 10600

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0459 AC: 3120 AN: 68026

Other (OTH) AF: 0.0374 AC: 79 AN: 2110

Alfa AF: 0.0376 Hom.: 11

Bravo AF: 0.0293

Asia WGS AF: 0.00577 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs72844458; hg19: chr2-85764027;