chr2-219629286-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_005070.4(SLC4A3):c.360C>T(p.Ser120=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000918 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00060 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00095 ( 0 hom. )
Consequence
SLC4A3
NM_005070.4 synonymous
NM_005070.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -7.36
Genes affected
SLC4A3 (HGNC:11029): (solute carrier family 4 member 3) The protein encoded by this gene is a plasma membrane anion exchange protein. The encoded protein has been found in brain, heart, kidney, small intestine, and lung. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
?
Variant 2-219629286-C-T is Benign according to our data. Variant chr2-219629286-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651938.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd at 93 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A3 | NM_005070.4 | c.360C>T | p.Ser120= | synonymous_variant | 4/23 | ENST00000358055.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A3 | ENST00000358055.8 | c.360C>T | p.Ser120= | synonymous_variant | 4/23 | 1 | NM_005070.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000611 AC: 93AN: 152182Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000894 AC: 223AN: 249538Hom.: 0 AF XY: 0.00102 AC XY: 138AN XY: 135260
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GnomAD4 exome AF: 0.000950 AC: 1389AN: 1461604Hom.: 0 Cov.: 34 AF XY: 0.000959 AC XY: 697AN XY: 727102
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GnomAD4 genome ? AF: 0.000604 AC: 92AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000551 AC XY: 41AN XY: 74468
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SLC4A3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 29, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | SLC4A3: BS1 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 22
Find out detailed SpliceAI scores and Pangolin per-transcript scores at