chr15-83067093-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025238.4(BTBD1):c.59C>T(p.Pro20Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,514,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025238.4 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 |
---|---|---|---|---|---|---|---|
BTBD1 | NM_025238.4 | c.59C>T | p.Pro20Leu | missense_variant | 1/8 | ENST00000261721.9 | |
BTBD1 | NM_001011885.2 | c.59C>T | p.Pro20Leu | missense_variant | 1/7 | ||
BTBD1 | XR_007064459.1 | n.160C>T | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTBD1 | ENST00000261721.9 | c.59C>T | p.Pro20Leu | missense_variant | 1/8 | 1 | NM_025238.4 | P1 | |
ENST00000566841.1 | n.735-36331G>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000568441.1 | n.38-23228G>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
BTBD1 | ENST00000379403.2 | c.59C>T | p.Pro20Leu | missense_variant | 1/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000166 AC: 2AN: 120392Hom.: 0 AF XY: 0.0000145 AC XY: 1AN XY: 69024
GnomAD4 exome AF: 0.00000294 AC: 4AN: 1362822Hom.: 0 Cov.: 37 AF XY: 0.00000445 AC XY: 3AN XY: 674678
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152044Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.59C>T (p.P20L) alteration is located in exon 1 (coding exon 1) of the BTBD1 gene. This alteration results from a C to T substitution at nucleotide position 59, causing the proline (P) at amino acid position 20 to be replaced by a leucine (L). 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