Genetic Variant PSMC1P4:n.872T>A (chr5-56275759-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000515236.1(PSMC1P4):n.872T>A variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PSMC1P4
ENST00000515236.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.79

Publications

6 publications found

Variant links:

Genes affected

PSMC1P4 (HGNC:39779): (proteasome 26S subunit, ATPase 1 pseudogene 4)

PSMC1P4 links:

ENSG00000308414 (HGNC:):

ENSG00000308414 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515236.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMC1P4	ENST00000515236.1	TSL:6	n.872T>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000308414	ENST00000833855.1		n.85-5374T>A		intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

815284

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

431732

African (AFR)

AF:

0.00

AC:

AN:

21032

American (AMR)

AF:

0.00

AC:

AN:

43320

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21886

East Asian (EAS)

AF:

0.00

AC:

AN:

36816

South Asian (SAS)

AF:

0.00

AC:

AN:

72834

European-Finnish (FIN)

AF:

0.00

AC:

AN:

46648

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3646

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

529880

Other (OTH)

AF:

0.00

AC:

AN:

39222

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.54

(source)

DANN

Benign

0.28

PhyloP100

3.8

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over