1-67420185-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001018069.2(SERBP1):c.775G>A(p.Glu259Lys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,605,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 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.775G>A | p.Glu259Lys | missense_variant, splice_region_variant | 6/8 | ENST00000361219.11 | |
SERBP1 | NM_001018067.2 | c.820G>A | p.Glu274Lys | missense_variant, splice_region_variant | 6/8 | ||
SERBP1 | NM_001018068.2 | c.802G>A | p.Glu268Lys | missense_variant, splice_region_variant | 6/8 | ||
SERBP1 | NM_015640.4 | c.757G>A | p.Glu253Lys | missense_variant, splice_region_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERBP1 | ENST00000361219.11 | c.775G>A | p.Glu259Lys | missense_variant, splice_region_variant | 6/8 | 1 | NM_001018069.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243338Hom.: 0 AF XY: 0.00000759 AC XY: 1AN XY: 131708
GnomAD4 exome AF: 0.00000551 AC: 8AN: 1452958Hom.: 0 Cov.: 30 AF XY: 0.00000830 AC XY: 6AN XY: 722566
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.820G>A (p.E274K) alteration is located in exon 6 (coding exon 6) of the SERBP1 gene. This alteration results from a G to A substitution at nucleotide position 820, causing the glutamic acid (E) at amino acid position 274 to be replaced by a lysine (K). 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