5-173151572-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_013979.3(BNIP1):c.184C>T(p.Leu62Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013979.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BNIP1 | ENST00000231668.13 | c.184C>T | p.Leu62Phe | missense_variant | Exon 3 of 7 | 1 | ENSP00000231668.9 | |||
BNIP1 | ENST00000352523.10 | c.184C>T | p.Leu62Phe | missense_variant | Exon 3 of 6 | 1 | ENSP00000239214.8 | |||
BNIP1 | ENST00000351486.10 | c.178-2750C>T | intron_variant | Intron 2 of 5 | 1 | NM_001205.3 | ENSP00000239215.7 | |||
BNIP1 | ENST00000393770.4 | c.178-2750C>T | intron_variant | Intron 2 of 4 | 1 | ENSP00000377365.4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 144676Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000892 AC: 2AN: 224254Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121600
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000922 AC: 13AN: 1409944Hom.: 0 Cov.: 35 AF XY: 0.00000570 AC XY: 4AN XY: 701426
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 144676Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 69974
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.184C>T (p.L62F) alteration is located in exon 3 (coding exon 3) of the BNIP1 gene. This alteration results from a C to T substitution at nucleotide position 184, causing the leucine (L) at amino acid position 62 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at