14-96263735-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000710.4(BDKRB1):āc.53T>Cā(p.Leu18Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_000710.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDKRB1 | NM_000710.4 | c.53T>C | p.Leu18Pro | missense_variant | 3/3 | ENST00000216629.11 | |
LOC124903375 | XR_007064322.1 | n.213-3843A>G | intron_variant, non_coding_transcript_variant | ||||
BDKRB1 | NM_001386007.1 | c.53T>C | p.Leu18Pro | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDKRB1 | ENST00000216629.11 | c.53T>C | p.Leu18Pro | missense_variant | 3/3 | 1 | NM_000710.4 | P1 | |
BDKRB1 | ENST00000553356.1 | c.53T>C | p.Leu18Pro | missense_variant | 3/5 | 1 | |||
ENST00000553638.1 | n.257-3843A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
BDKRB1 | ENST00000611804.1 | c.53T>C | p.Leu18Pro | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251380Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135878
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461872Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727240
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 16, 2024 | The c.53T>C (p.L18P) alteration is located in exon 3 (coding exon 1) of the BDKRB1 gene. This alteration results from a T to C substitution at nucleotide position 53, causing the leucine (L) at amino acid position 18 to be replaced by a proline (P). 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