1-67425221-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001018069.2(SERBP1):c.467C>T(p.Pro156Leu) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000815 in 1,594,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001018069.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERBP1 | NM_001018069.2 | c.467C>T | p.Pro156Leu | missense_variant, splice_region_variant | 3/8 | ENST00000361219.11 | |
SERBP1 | NM_001018067.2 | c.467C>T | p.Pro156Leu | missense_variant, splice_region_variant | 3/8 | ||
SERBP1 | NM_001018068.2 | c.467C>T | p.Pro156Leu | missense_variant, splice_region_variant | 3/8 | ||
SERBP1 | NM_015640.4 | c.467C>T | p.Pro156Leu | missense_variant, splice_region_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERBP1 | ENST00000361219.11 | c.467C>T | p.Pro156Leu | missense_variant, splice_region_variant | 3/8 | 1 | NM_001018069.2 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151844Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000429 AC: 1AN: 232856Hom.: 0 AF XY: 0.00000792 AC XY: 1AN XY: 126330
GnomAD4 exome AF: 0.00000693 AC: 10AN: 1442694Hom.: 0 Cov.: 32 AF XY: 0.00000697 AC XY: 5AN XY: 717358
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151844Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74124
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | The c.467C>T (p.P156L) alteration is located in exon 3 (coding exon 3) of the SERBP1 gene. This alteration results from a C to T substitution at nucleotide position 467, causing the proline (P) at amino acid position 156 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