19-49430690-G-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_020309.4(SLC17A7):c.1512C>T(p.Ser504=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000537 in 1,614,060 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00029 ( 2 hom. )
Consequence
SLC17A7
NM_020309.4 synonymous
NM_020309.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.440
Genes affected
SLC17A7 (HGNC:16704): (solute carrier family 17 member 7) The protein encoded by this gene is a vesicle-bound, sodium-dependent phosphate transporter that is specifically expressed in the neuron-rich regions of the brain. It is preferentially associated with the membranes of synaptic vesicles and functions in glutamate transport. The protein shares 82% identity with the differentiation-associated Na-dependent inorganic phosphate cotransporter and they appear to form a distinct class within the Na+/Pi cotransporter family. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 19-49430690-G-A is Benign according to our data. Variant chr19-49430690-G-A is described in ClinVar as [Benign]. Clinvar id is 727740.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.44 with no splicing effect.
BS2
High AC in GnomAd4 at 445 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC17A7 | NM_020309.4 | c.1512C>T | p.Ser504= | synonymous_variant | 12/12 | ENST00000221485.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC17A7 | ENST00000221485.8 | c.1512C>T | p.Ser504= | synonymous_variant | 12/12 | 1 | NM_020309.4 | P1 | |
SLC17A7 | ENST00000600601.5 | c.1311C>T | p.Ser437= | synonymous_variant | 12/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00293 AC: 445AN: 152068Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000774 AC: 194AN: 250726Hom.: 0 AF XY: 0.000523 AC XY: 71AN XY: 135752
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GnomAD4 exome AF: 0.000288 AC: 421AN: 1461874Hom.: 2 Cov.: 33 AF XY: 0.000219 AC XY: 159AN XY: 727248
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GnomAD4 genome AF: 0.00292 AC: 445AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00302 AC XY: 225AN XY: 74398
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 13, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at