rs1057058
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BS1BS2
The NM_004330.4(BNIP2):c.507G>A(p.Val169=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 1,612,956 control chromosomes in the GnomAD database, including 865 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 0.021 ( 58 hom., cov: 33)
Exomes 𝑓: 0.030 ( 807 hom. )
Consequence
BNIP2
NM_004330.4 synonymous
NM_004330.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.490
Genes affected
BNIP2 (HGNC:1083): (BCL2 interacting protein 2) This gene is a member of the BCL2/adenovirus E1B 19 kd-interacting protein (BNIP) family. It interacts with the E1B 19 kDa protein, which protects cells from virally-induced cell death. The encoded protein also interacts with E1B 19 kDa-like sequences of BCL2, another apoptotic protector. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.27).
BP7
?
Synonymous conserved (PhyloP=0.49 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0212 (3222/152200) while in subpopulation NFE AF= 0.0335 (2278/67996). AF 95% confidence interval is 0.0324. There are 58 homozygotes in gnomad4. There are 1496 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 58 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BNIP2 | NM_004330.4 | c.507G>A | p.Val169= | synonymous_variant | 6/10 | ENST00000607373.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BNIP2 | ENST00000607373.6 | c.507G>A | p.Val169= | synonymous_variant | 6/10 | 1 | NM_004330.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0212 AC: 3224AN: 152082Hom.: 58 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0215 AC: 5389AN: 250976Hom.: 96 AF XY: 0.0214 AC XY: 2898AN XY: 135642
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GnomAD4 exome AF: 0.0304 AC: 44342AN: 1460756Hom.: 807 Cov.: 31 AF XY: 0.0297 AC XY: 21585AN XY: 726672
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GnomAD4 genome ? AF: 0.0212 AC: 3222AN: 152200Hom.: 58 Cov.: 33 AF XY: 0.0201 AC XY: 1496AN XY: 74408
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at