14-96263783-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000710.4(BDKRB1):c.101A>T(p.Asp34Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000954 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.101A>T | p.Asp34Val | missense_variant | 3/3 | ENST00000216629.11 | |
LOC124903375 | XR_007064322.1 | n.213-3891T>A | intron_variant, non_coding_transcript_variant | ||||
BDKRB1 | NM_001386007.1 | c.101A>T | p.Asp34Val | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDKRB1 | ENST00000216629.11 | c.101A>T | p.Asp34Val | missense_variant | 3/3 | 1 | NM_000710.4 | P1 | |
BDKRB1 | ENST00000553356.1 | c.101A>T | p.Asp34Val | missense_variant | 3/5 | 1 | |||
ENST00000553638.1 | n.257-3891T>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
BDKRB1 | ENST00000611804.1 | c.101A>T | p.Asp34Val | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251438Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135908
GnomAD4 exome AF: 0.0000971 AC: 142AN: 1461882Hom.: 0 Cov.: 30 AF XY: 0.0000949 AC XY: 69AN XY: 727246
GnomAD4 genome ? AF: 0.0000789 AC: 12AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 28, 2023 | The c.101A>T (p.D34V) alteration is located in exon 3 (coding exon 1) of the BDKRB1 gene. This alteration results from a A to T substitution at nucleotide position 101, causing the aspartic acid (D) at amino acid position 34 to be replaced by a valine (V). 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