chr19-17872340-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000453.3(SLC5A5):c.21G>A(p.Gly7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,430,778 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: not found (cov: 33)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
SLC5A5
NM_000453.3 synonymous
NM_000453.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.355
Genes affected
SLC5A5 (HGNC:11040): (solute carrier family 5 member 5) This gene encodes a member of the sodium glucose cotransporter family. The encoded protein is responsible for the uptake of iodine in tissues such as the thyroid and lactating breast tissue. The iodine taken up by the thyroid is incorporated into the metabolic regulators triiodothyronine (T3) and tetraiodothyronine (T4). Mutations in this gene are associated with thyroid dyshormonogenesis 1.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 19-17872340-G-A is Benign according to our data. Variant chr19-17872340-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2956599.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.355 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC5A5 | NM_000453.3 | c.21G>A | p.Gly7= | synonymous_variant | 1/15 | ENST00000222248.4 | |
SLC5A5 | XM_011528192.3 | c.21G>A | p.Gly7= | synonymous_variant | 1/15 | ||
SLC5A5 | XM_011528193.4 | c.-51-196G>A | intron_variant | ||||
SLC5A5 | XM_017027158.2 | c.-51-196G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC5A5 | ENST00000222248.4 | c.21G>A | p.Gly7= | synonymous_variant | 1/15 | 1 | NM_000453.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.0000100 AC: 2AN: 199618Hom.: 0 AF XY: 0.00000920 AC XY: 1AN XY: 108694
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GnomAD4 exome AF: 0.0000133 AC: 19AN: 1430778Hom.: 0 Cov.: 33 AF XY: 0.0000169 AC XY: 12AN XY: 708858
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GnomAD4 genome ? Cov.: 33
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at