X-15750100-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007220.4(CA5B):c.77C>T(p.Pro26Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,210,028 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007220.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA5B | NM_007220.4 | c.77C>T | p.Pro26Leu | missense_variant | Exon 2 of 8 | ENST00000318636.8 | NP_009151.1 | |
CA5BP1-CA5B | NR_160544.1 | n.841C>T | non_coding_transcript_exon_variant | Exon 5 of 12 | ||||
CA5BP1-CA5B | NR_160545.1 | n.841C>T | non_coding_transcript_exon_variant | Exon 5 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111997Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34169
GnomAD3 exomes AF: 0.0000436 AC: 8AN: 183425Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67861
GnomAD4 exome AF: 0.0000282 AC: 31AN: 1098031Hom.: 0 Cov.: 29 AF XY: 0.0000275 AC XY: 10AN XY: 363387
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111997Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34169
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.77C>T (p.P26L) alteration is located in exon 2 (coding exon 1) of the CA5B gene. This alteration results from a C to T substitution at nucleotide position 77, causing the proline (P) at amino acid position 26 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