2-85537843-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_038942.1(PARTICL):​n.1044T>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 0.298 in 151,782 control chromosomes in the GnomAD database, including 6,942 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 ( 6942 hom., cov: 32)

Consequence

PARTICL
NR_038942.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364
Variant links:
Genes affected
PARTICL (HGNC:50886): (promoter of MAT2A antisense radiation-induced circulating long non-coding RNA)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
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
PARTICLNR_038942.1 linkn.1044T>A non_coding_transcript_exon_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PARTICLENST00000667933.2 linkn.941T>A non_coding_transcript_exon_variant Exon 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.298
AC:
45187
AN:
151664
Hom.:
6930
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.365
Gnomad AMI
AF:
0.346
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:
0.239
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:
45226
AN:
151782
Hom.:
6942
Cov.:
32
AF XY:
0.296
AC XY:
21949
AN XY:
74178
show subpopulations
Gnomad4 AFR
AF:
0.365
Gnomad4 AMR
AF:
0.227
Gnomad4 ASJ
AF:
0.215
Gnomad4 EAS
AF:
0.323
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.319
Gnomad4 NFE
AF:
0.281
Gnomad4 OTH
AF:
0.287
Alfa
AF:
0.270
Hom.:
755
Bravo
AF:
0.299
Asia WGS
AF:
0.277
AC:
964
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.91
DANN
Benign
0.76

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1048740; hg19: chr2-85764966; API