chr11-117820690-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001680.5(FXYD2):c.183C>T(p.Ile61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,950 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 0.00014 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000040 ( 0 hom. )
Consequence
FXYD2
NM_001680.5 synonymous
NM_001680.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0960
Genes affected
FXYD2 (HGNC:4026): (FXYD domain containing ion transport regulator 2) This gene encodes a member of the FXYD family of transmembrane proteins. This particular protein encodes the sodium/potassium-transporting ATPase subunit gamma. Mutations in this gene have been associated with Renal Hypomagnesemia-2. Alternatively spliced transcript variants have been described. Read-through transcripts have been observed between this locus and the upstream FXYD domain-containing ion transport regulator 6 (FXYD6, GeneID 53826) locus.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 11-117820690-G-A is Benign according to our data. Variant chr11-117820690-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 302523.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.096 with no splicing effect.
BS2
High AC in GnomAd4 at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXYD2 | NM_001680.5 | c.183C>T | p.Ile61= | synonymous_variant | 5/6 | ENST00000292079.7 | |
FXYD6-FXYD2 | NM_001243598.4 | c.*16C>T | 3_prime_UTR_variant | 9/10 | |||
FXYD6-FXYD2 | NM_001204268.3 | c.417C>T | p.Ile139= | synonymous_variant | 10/11 | ||
FXYD2 | NM_021603.4 | c.177C>T | p.Ile59= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXYD2 | ENST00000292079.7 | c.183C>T | p.Ile61= | synonymous_variant | 5/6 | 1 | NM_001680.5 | ||
ENST00000531850.2 | n.506G>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152060Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000104 AC: 26AN: 250986Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135702
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GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461772Hom.: 0 Cov.: 33 AF XY: 0.0000440 AC XY: 32AN XY: 727194
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152178Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74402
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Renal hypomagnesemia 2 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 21, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 12, 2023 | - - |
Computational scores
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at