chr2-219630127-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The ENST00000273063.10(SLC4A3):c.667C>T(p.Pro223Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000473 in 1,611,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000273063.10 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A3 | NM_005070.4 | c.612-26C>T | intron_variant | ENST00000358055.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A3 | ENST00000358055.8 | c.612-26C>T | intron_variant | 1 | NM_005070.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000947 AC: 144AN: 152064Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000601 AC: 146AN: 242766Hom.: 0 AF XY: 0.000644 AC XY: 85AN XY: 131894
GnomAD4 exome AF: 0.000424 AC: 619AN: 1459814Hom.: 0 Cov.: 33 AF XY: 0.000471 AC XY: 342AN XY: 726044
GnomAD4 genome ? AF: 0.000947 AC: 144AN: 152064Hom.: 0 Cov.: 31 AF XY: 0.000956 AC XY: 71AN XY: 74276
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 30, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at