chr11-117820548-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 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_single_submitter, 1 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 GnomAd at 2230 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
GnomAD3 genomes
?
AF:
AC:
2230
AN:
152202
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00567 AC: 6508AN: 1148196Hom.: 66 Cov.: 15 AF XY: 0.00577 AC XY: 3336AN XY: 577774
GnomAD4 exome
AF:
AC:
6508
AN:
1148196
Hom.:
Cov.:
15
AF XY:
AC XY:
3336
AN XY:
577774
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0147 AC: 2234AN: 152320Hom.: 32 Cov.: 32 AF XY: 0.0144 AC XY: 1072AN XY: 74472
GnomAD4 genome
?
AF:
AC:
2234
AN:
152320
Hom.:
Cov.:
32
AF XY:
AC XY:
1072
AN XY:
74472
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
15
AN:
3478
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 | GeneDx | Nov 08, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
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