Genetic Variant PSMD3-AS1:n.2389A>G (chr17-40010626-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_198981.1(PSMD3-AS1):n.2389A>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 0.359 in 152,144 control chromosomes in the GnomAD database, including 9,952 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 0.36 ( 9952 hom., cov: 33)

Consequence

PSMD3-AS1
NR_198981.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.273

Publications

52 publications found

Variant links:

Genes affected

PSMD3-AS1 (HGNC:58140):

PSMD3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PSMD3-AS1	NR_198981.1 link	n.2389A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265799	ENST00000801108.1 link	n.537+1936A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54538

AN:

152024

Hom.:

9935

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.422

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.461

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.337

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

GnomAD4 genome

AF:

0.359

AC:

54618

AN:

152144

Hom.:

9952

Cov.:

AF XY:

0.357

AC XY:

26562

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.302

AC:

12536

AN:

41516

American (AMR)

AF:

0.346

AC:

5297

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.349

AC:

1211

AN:

3472

East Asian (EAS)

AF:

0.461

AC:

2385

AN:

5176

South Asian (SAS)

AF:

0.253

AC:

1218

AN:

4822

European-Finnish (FIN)

AF:

0.397

AC:

4190

AN:

10564

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26607

AN:

67990

Other (OTH)

AF:

0.340

AC:

717

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1834

3668

5502

7336

9170

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.373

Hom.:

37878

Bravo

AF:

0.353

Asia WGS

AF:

0.373

AC:

1294

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.3

(source)

DANN

Benign

0.62

PhyloP100

0.27

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over