Variant rs12325114 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000569389.5(PSMD7-DT):n.129+26631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,106 control chromosomes in the GnomAD database, including 1,468 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 0.14 ( 1468 hom., cov: 32)

Consequence

PSMD7-DT
ENST00000569389.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.428

Variant links:

Genes affected

PSMD7-DT (HGNC:53056): (PSMD7 divergent transcript)

PSMD7-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
PSMD7-DT	ENST00000562888.1 link	n.348+26423A>G	intron_variant	5
PSMD7-DT	ENST00000569389.5 link	n.129+26631A>G	intron_variant	3
PSMD7-DT	ENST00000641277.1 link	n.111+26431A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.137

AC:

20871

AN:

151988

Hom.:

1467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.232

Gnomad SAS

AF:

0.0757

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.134

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.136

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

GnomAD4 genome

AF:

0.137

AC:

20886

AN:

152106

Hom.:

1468

Cov.:

AF XY:

0.138

AC XY:

10279

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0999

Gnomad4 AMR

AF:

0.146

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.0751

Gnomad4 FIN

AF:

0.203

Gnomad4 NFE

AF:

0.140

Gnomad4 OTH

AF:

0.140

Alfa

AF:

0.100

Hom.:

238

Bravo

AF:

0.135

Asia WGS

AF:

0.190

AC:

663

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.0

DANN

Benign

0.34

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over