1-154945758-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020524.4(PBXIP1):c.1916C>T(p.Ser639Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,870 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 (★).
Frequency
Consequence
NM_020524.4 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 |
---|---|---|---|---|---|---|---|
PBXIP1 | NM_020524.4 | c.1916C>T | p.Ser639Leu | missense_variant | 10/11 | ENST00000368463.8 | |
PBXIP1 | NM_001317734.2 | c.1829C>T | p.Ser610Leu | missense_variant | 9/10 | ||
PBXIP1 | NM_001317735.2 | c.1451C>T | p.Ser484Leu | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBXIP1 | ENST00000368463.8 | c.1916C>T | p.Ser639Leu | missense_variant | 10/11 | 1 | NM_020524.4 | P2 | |
PBXIP1 | ENST00000368465.5 | c.1829C>T | p.Ser610Leu | missense_variant | 9/10 | 2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249784Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135128
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461870Hom.: 0 Cov.: 34 AF XY: 0.00000550 AC XY: 4AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at