19-1986859-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017797.4(BTBD2):c.1387G>A(p.Val463Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000267 in 1,459,378 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_017797.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BTBD2 | ENST00000255608.9 | c.1387G>A | p.Val463Ile | missense_variant | Exon 8 of 9 | 1 | NM_017797.4 | ENSP00000255608.3 | ||
BTBD2 | ENST00000589685.2 | n.1181G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 1 | |||||
BTBD2 | ENST00000592895.5 | n.1522G>A | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 | |||||
BTBD2 | ENST00000592082.5 | c.*105G>A | downstream_gene_variant | 5 | ENSP00000481163.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249040Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134798
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1459378Hom.: 0 Cov.: 34 AF XY: 0.0000386 AC XY: 28AN XY: 725898
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1387G>A (p.V463I) alteration is located in exon 8 (coding exon 8) of the BTBD2 gene. This alteration results from a G to A substitution at nucleotide position 1387, causing the valine (V) at amino acid position 463 to be replaced by an isoleucine (I). 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