chr2-219628427-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_005070.4(SLC4A3):c.74C>G(p.Pro25Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00014 in 1,612,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P25T) has been classified as Uncertain significance.
Frequency
Consequence
NM_005070.4 missense
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 |
---|---|---|---|---|---|---|---|
SLC4A3 | NM_005070.4 | c.74C>G | p.Pro25Arg | missense_variant | 3/23 | ENST00000358055.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A3 | ENST00000358055.8 | c.74C>G | p.Pro25Arg | missense_variant | 3/23 | 1 | NM_005070.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 151962Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000125 AC: 31AN: 247860Hom.: 0 AF XY: 0.000112 AC XY: 15AN XY: 134306
GnomAD4 exome AF: 0.000143 AC: 209AN: 1460784Hom.: 0 Cov.: 31 AF XY: 0.000149 AC XY: 108AN XY: 726652
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 151962Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74196
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2022 | The c.74C>G (p.P25R) alteration is located in exon 3 (coding exon 2) of the SLC4A3 gene. This alteration results from a C to G substitution at nucleotide position 74, causing the proline (P) at amino acid position 25 to be replaced by an arginine (R). 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