chr11-117820637-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001680.5(FXYD2):c.*6+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,613,456 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0022 ( 11 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 52 hom. )
Consequence
FXYD2
NM_001680.5 intron
NM_001680.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.158
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 11-117820637-C-T is Benign according to our data. Variant chr11-117820637-C-T is described in ClinVar as [Benign]. Clinvar id is 1248580.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0519 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXYD2 | NM_001680.5 | c.*6+29G>A | intron_variant | ENST00000292079.7 | |||
FXYD6-FXYD2 | NM_001243598.4 | c.*40+29G>A | intron_variant | ||||
FXYD6-FXYD2 | NM_001204268.3 | c.*6+29G>A | intron_variant | ||||
FXYD2 | NM_021603.4 | c.*6+29G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXYD2 | ENST00000292079.7 | c.*6+29G>A | intron_variant | 1 | NM_001680.5 | ||||
ENST00000531850.2 | n.453C>T | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00224 AC: 341AN: 152154Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00447 AC: 1120AN: 250342Hom.: 32 AF XY: 0.00407 AC XY: 551AN XY: 135386
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GnomAD4 exome AF: 0.00156 AC: 2273AN: 1461184Hom.: 52 Cov.: 31 AF XY: 0.00151 AC XY: 1096AN XY: 726940
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GnomAD4 genome AF: 0.00223 AC: 339AN: 152272Hom.: 11 Cov.: 32 AF XY: 0.00239 AC XY: 178AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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