chr2-219629227-A-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_005070.4(SLC4A3):c.301A>C(p.Thr101Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,460,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A3 | NM_005070.4 | c.301A>C | p.Thr101Pro | missense_variant | 4/23 | ENST00000358055.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A3 | ENST00000358055.8 | c.301A>C | p.Thr101Pro | missense_variant | 4/23 | 1 | NM_005070.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 245842Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134022
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460686Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 726696
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | The c.301A>C (p.T101P) alteration is located in exon 4 (coding exon 3) of the SLC4A3 gene. This alteration results from a A to C substitution at nucleotide position 301, causing the threonine (T) at amino acid position 101 to be replaced by a proline (P). 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