chr8-56441821-T-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001135690.3(PENK):āc.255A>Gā(p.Arg85=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000242 in 1,614,234 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0014 ( 0 hom., cov: 32)
Exomes š: 0.00012 ( 0 hom. )
Consequence
PENK
NM_001135690.3 synonymous
NM_001135690.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0940
Genes affected
PENK (HGNC:8831): (proenkephalin) This gene encodes a preproprotein that is proteolytically processed to generate multiple protein products. These products include the pentapeptide opioids Met-enkephalin and Leu-enkephalin, which are stored in synaptic vesicles, then released into the synapse where they bind to mu- and delta-opioid receptors to modulate the perception of pain. Other non-opioid cleavage products may function in distinct biological activities. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 8-56441821-T-C is Benign according to our data. Variant chr8-56441821-T-C is described in ClinVar as [Benign]. Clinvar id is 720657.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.094 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PENK | NM_001135690.3 | c.255A>G | p.Arg85= | synonymous_variant | 4/4 | ENST00000451791.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PENK | ENST00000451791.7 | c.255A>G | p.Arg85= | synonymous_variant | 4/4 | 1 | NM_001135690.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00140 AC: 213AN: 152226Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000402 AC: 101AN: 251482Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135916
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GnomAD4 exome AF: 0.000121 AC: 177AN: 1461890Hom.: 0 Cov.: 33 AF XY: 0.0000880 AC XY: 64AN XY: 727248
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GnomAD4 genome AF: 0.00140 AC: 213AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.00122 AC XY: 91AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at