1-200848493-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_203459.4(CAMSAP2):āc.1724T>Cā(p.Met575Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,612,994 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 (ā ).
Frequency
Consequence
NM_203459.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CAMSAP2 | NM_203459.4 | c.1724T>C | p.Met575Thr | missense_variant | 11/17 | ENST00000358823.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CAMSAP2 | ENST00000358823.7 | c.1724T>C | p.Met575Thr | missense_variant | 11/17 | 5 | NM_203459.4 | P3 | |
CAMSAP2 | ENST00000236925.8 | c.1757T>C | p.Met586Thr | missense_variant | 12/18 | 1 | |||
CAMSAP2 | ENST00000413307.6 | c.1676T>C | p.Met559Thr | missense_variant | 11/17 | 1 | A2 | ||
CAMSAP2 | ENST00000447701.2 | c.395+1201T>C | intron_variant, NMD_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250212Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135350
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460698Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 726664
GnomAD4 genome AF: 0.000131 AC: 20AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.1724T>C (p.M575T) alteration is located in exon 11 (coding exon 11) of the CAMSAP2 gene. This alteration results from a T to C substitution at nucleotide position 1724, causing the methionine (M) at amino acid position 575 to be replaced by a threonine (T). 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