chr2-219628514-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_005070.4(SLC4A3):c.161C>T(p.Pro54Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,613,652 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005070.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A3 | NM_005070.4 | c.161C>T | p.Pro54Leu | missense_variant | 3/23 | ENST00000358055.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A3 | ENST00000358055.8 | c.161C>T | p.Pro54Leu | missense_variant | 3/23 | 1 | NM_005070.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0105 AC: 1594AN: 152074Hom.: 21 Cov.: 31
GnomAD3 exomes AF: 0.00275 AC: 688AN: 249808Hom.: 11 AF XY: 0.00199 AC XY: 269AN XY: 135356
GnomAD4 exome AF: 0.00102 AC: 1488AN: 1461460Hom.: 23 Cov.: 31 AF XY: 0.000820 AC XY: 596AN XY: 727036
GnomAD4 genome ? AF: 0.0105 AC: 1597AN: 152192Hom.: 21 Cov.: 31 AF XY: 0.00987 AC XY: 734AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at