6-17507310-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006366.3(CAP2):āc.442G>Cā(p.Val148Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,840 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006366.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAP2 | NM_006366.3 | c.442G>C | p.Val148Leu | missense_variant, splice_region_variant | 5/13 | ENST00000229922.7 | NP_006357.1 | |
CAP2 | NM_001363534.2 | c.364G>C | p.Val122Leu | missense_variant, splice_region_variant | 4/12 | NP_001350463.1 | ||
CAP2 | NM_001363533.2 | c.301-31959G>C | intron_variant | NP_001350462.1 | ||||
LOC101928491 | NR_110855.1 | n.282+1263C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAP2 | ENST00000229922.7 | c.442G>C | p.Val148Leu | missense_variant, splice_region_variant | 5/13 | 1 | NM_006366.3 | ENSP00000229922.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251368Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135848
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461840Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727226
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 23, 2022 | The c.442G>C (p.V148L) alteration is located in exon 5 (coding exon 4) of the CAP2 gene. This alteration results from a G to C substitution at nucleotide position 442, causing the valine (V) at amino acid position 148 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