GeneBe

rs762872468

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4

The NM_001136239.4(PRDM6):​c.172_177delCCCCCG​(p.Pro58_Pro59del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000225 in 1,335,636 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000022 ( 0 hom. )

Consequence

PRDM6
NM_001136239.4 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.36

Publications

0 publications found
Variant links:
Genes affected
PRDM6 (HGNC:9350): (PR/SET domain 6) The protein encoded by this gene is a transcriptional repressor and a member of the PRDM family. Family members contain a PR domain and multiple zinc-finger domains. The encoded protein is involved in regulation of vascular smooth muscle cells (VSMC) contractile proteins. Mutations in this gene result in patent ductus arteriosus 3 (PDA3). [provided by RefSeq, Apr 2017]
PRDM6-AS1 (HGNC:55869): (PRDM6 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001136239.4.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136239.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRDM6
NM_001136239.4
MANE Select
c.172_177delCCCCCGp.Pro58_Pro59del
conservative_inframe_deletion
Exon 2 of 8NP_001129711.1Q9NQX0-3
PRDM6-AS1
NR_146771.1
n.135_140delGGGCGG
non_coding_transcript_exon
Exon 1 of 2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PRDM6
ENST00000407847.5
TSL:5 MANE Select
c.172_177delCCCCCGp.Pro58_Pro59del
conservative_inframe_deletion
Exon 2 of 8ENSP00000384725.3Q9NQX0-3
PRDM6
ENST00000890813.1
c.172_177delCCCCCGp.Pro58_Pro59del
conservative_inframe_deletion
Exon 1 of 7ENSP00000560872.1
PRDM6-AS1
ENST00000458103.3
TSL:2
n.118_123delGGGCGG
non_coding_transcript_exon
Exon 1 of 2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000225
AC:
3
AN:
1335636
Hom.:
0
AF XY:
0.00000304
AC XY:
2
AN XY:
658152
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
26492
American (AMR)
AF:
0.00
AC:
0
AN:
27012
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
22786
East Asian (EAS)
AF:
0.00
AC:
0
AN:
28962
South Asian (SAS)
AF:
0.0000139
AC:
1
AN:
72156
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
44104
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4294
European-Non Finnish (NFE)
AF:
0.00000190
AC:
2
AN:
1054718
Other (OTH)
AF:
0.00
AC:
0
AN:
55112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.542
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
3.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs762872468; hg19: chr5-122425871; API