chr2-219629653-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_005070.4(SLC4A3):c.569C>T(p.Ser190Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,613,312 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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 Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A3 | NM_005070.4 | c.569C>T | p.Ser190Leu | missense_variant | 5/23 | ENST00000358055.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A3 | ENST00000358055.8 | c.569C>T | p.Ser190Leu | missense_variant | 5/23 | 1 | NM_005070.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152054Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000244 AC: 61AN: 249816Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135392
GnomAD4 exome AF: 0.000199 AC: 291AN: 1461140Hom.: 1 Cov.: 32 AF XY: 0.000249 AC XY: 181AN XY: 726894
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152172Hom.: 0 Cov.: 30 AF XY: 0.000148 AC XY: 11AN XY: 74390
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.569C>T (p.S190L) alteration is located in exon 5 (coding exon 4) of the SLC4A3 gene. This alteration results from a C to T substitution at nucleotide position 569, causing the serine (S) at amino acid position 190 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