chr7-103119720-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001122838.3(NAPEPLD):c.798A>G(p.Leu266=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,614,154 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0068 ( 24 hom., cov: 32)
Exomes 𝑓: 0.00075 ( 20 hom. )
Consequence
NAPEPLD
NM_001122838.3 synonymous
NM_001122838.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.73
Genes affected
NAPEPLD (HGNC:21683): (N-acyl phosphatidylethanolamine phospholipase D) NAPEPLD is a phospholipase D type enzyme that catalyzes the release of N-acylethanolamine (NAE) from N-acyl-phosphatidylethanolamine (NAPE) in the second step of the biosynthesis of N-acylethanolamine (Okamoto et al., 2004 [PubMed 14634025]).[supplied by OMIM, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 7-103119720-T-C is Benign according to our data. Variant chr7-103119720-T-C is described in ClinVar as [Benign]. Clinvar id is 768191.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.73 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00677 (1031/152270) while in subpopulation AFR AF= 0.0235 (975/41548). AF 95% confidence interval is 0.0222. There are 24 homozygotes in gnomad4. There are 502 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAPEPLD | NM_001122838.3 | c.798A>G | p.Leu266= | synonymous_variant | 3/5 | ENST00000465647.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAPEPLD | ENST00000465647.6 | c.798A>G | p.Leu266= | synonymous_variant | 3/5 | 1 | NM_001122838.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00664 AC: 1011AN: 152152Hom.: 17 Cov.: 32
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GnomAD3 exomes AF: 0.00182 AC: 458AN: 251378Hom.: 6 AF XY: 0.00130 AC XY: 176AN XY: 135868
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GnomAD4 exome AF: 0.000753 AC: 1101AN: 1461884Hom.: 20 Cov.: 31 AF XY: 0.000681 AC XY: 495AN XY: 727242
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GnomAD4 genome ? AF: 0.00677 AC: 1031AN: 152270Hom.: 24 Cov.: 32 AF XY: 0.00674 AC XY: 502AN XY: 74456
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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 | May 09, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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