chr11-117820548-C-A
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001680.5(FXYD2):c.*6+118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 1,300,516 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.015 ( 32 hom., cov: 32)
Exomes 𝑓: 0.0057 ( 66 hom. )
Consequence
FXYD2
NM_001680.5 intron
NM_001680.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.317
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 -16 ACMG points.
BP6
Variant 11-117820548-C-A is Benign according to our data. Variant chr11-117820548-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1317355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0147 (2234/152320) while in subpopulation AFR AF= 0.037 (1536/41566). AF 95% confidence interval is 0.0354. There are 32 homozygotes in gnomad4. There are 1072 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2234 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXYD2 | NM_001680.5 | c.*6+118G>T | intron_variant | ENST00000292079.7 | |||
FXYD6-FXYD2 | NM_001243598.4 | c.*40+118G>T | intron_variant | ||||
FXYD6-FXYD2 | NM_001204268.3 | c.*6+118G>T | intron_variant | ||||
FXYD2 | NM_021603.4 | c.*6+118G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXYD2 | ENST00000292079.7 | c.*6+118G>T | intron_variant | 1 | NM_001680.5 | ||||
ENST00000531850.2 | n.364C>A | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0147 AC: 2230AN: 152202Hom.: 32 Cov.: 32
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GnomAD4 exome AF: 0.00567 AC: 6508AN: 1148196Hom.: 66 Cov.: 15 AF XY: 0.00577 AC XY: 3336AN XY: 577774
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GnomAD4 genome AF: 0.0147 AC: 2234AN: 152320Hom.: 32 Cov.: 32 AF XY: 0.0144 AC XY: 1072AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2020 | - - |
Computational scores
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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
DS_AG_spliceai
Position offset: -5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at