X-15750163-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_007220.4(CA5B):c.140C>T(p.Ala47Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000486 in 1,194,362 control chromosomes in the GnomAD database, including 1 homozygotes. There are 22 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007220.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CA5B | NM_007220.4 | c.140C>T | p.Ala47Val | missense_variant, splice_region_variant | Exon 2 of 8 | ENST00000318636.8 | NP_009151.1 | |
CA5BP1-CA5B | NR_160544.1 | n.904C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 5 of 12 | ||||
CA5BP1-CA5B | NR_160545.1 | n.904C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 5 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000713 AC: 8AN: 112222Hom.: 0 Cov.: 23 AF XY: 0.0000872 AC XY: 3AN XY: 34396
GnomAD3 exomes AF: 0.000118 AC: 21AN: 178689Hom.: 1 AF XY: 0.000110 AC XY: 7AN XY: 63625
GnomAD4 exome AF: 0.0000462 AC: 50AN: 1082140Hom.: 1 Cov.: 27 AF XY: 0.0000546 AC XY: 19AN XY: 348082
GnomAD4 genome AF: 0.0000713 AC: 8AN: 112222Hom.: 0 Cov.: 23 AF XY: 0.0000872 AC XY: 3AN XY: 34396
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.140C>T (p.A47V) 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 140, causing the alanine (A) at amino acid position 47 to be replaced by a valine (V). 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