chr11-117820430-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001680.5(FXYD2):​c.*7-58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 571,224 control chromosomes in the GnomAD database, including 118,923 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.58 ( 27428 hom., cov: 31)
Exomes 𝑓: 0.65 ( 91495 hom. )

Consequence

FXYD2
NM_001680.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -6.02
Variant links:
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=-0.9).
BP6
Variant 11-117820430-C-T is Benign according to our data. Variant chr11-117820430-C-T is described in ClinVar as [Benign]. Clinvar id is 1243897.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FXYD2NM_001680.5 linkuse as main transcriptc.*7-58G>A intron_variant ENST00000292079.7
FXYD6-FXYD2NM_001243598.4 linkuse as main transcriptc.*41-58G>A intron_variant
FXYD6-FXYD2NM_001204268.3 linkuse as main transcriptc.*7-58G>A intron_variant
FXYD2NM_021603.4 linkuse as main transcriptc.*7-58G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FXYD2ENST00000292079.7 linkuse as main transcriptc.*7-58G>A intron_variant 1 NM_001680.5 P54710-1
ENST00000531850.2 linkuse as main transcriptn.277-31C>T intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.584
AC:
88434
AN:
151380
Hom.:
27415
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.361
Gnomad AMI
AF:
0.556
Gnomad AMR
AF:
0.695
Gnomad ASJ
AF:
0.622
Gnomad EAS
AF:
0.673
Gnomad SAS
AF:
0.483
Gnomad FIN
AF:
0.740
Gnomad MID
AF:
0.563
Gnomad NFE
AF:
0.670
Gnomad OTH
AF:
0.581
GnomAD4 exome
AF:
0.654
AC:
274387
AN:
419728
Hom.:
91495
Cov.:
4
AF XY:
0.647
AC XY:
141812
AN XY:
219048
show subpopulations
Gnomad4 AFR exome
AF:
0.365
Gnomad4 AMR exome
AF:
0.752
Gnomad4 ASJ exome
AF:
0.623
Gnomad4 EAS exome
AF:
0.685
Gnomad4 SAS exome
AF:
0.492
Gnomad4 FIN exome
AF:
0.750
Gnomad4 NFE exome
AF:
0.673
Gnomad4 OTH exome
AF:
0.638
GnomAD4 genome
AF:
0.584
AC:
88471
AN:
151496
Hom.:
27428
Cov.:
31
AF XY:
0.588
AC XY:
43536
AN XY:
74012
show subpopulations
Gnomad4 AFR
AF:
0.361
Gnomad4 AMR
AF:
0.695
Gnomad4 ASJ
AF:
0.622
Gnomad4 EAS
AF:
0.673
Gnomad4 SAS
AF:
0.482
Gnomad4 FIN
AF:
0.740
Gnomad4 NFE
AF:
0.670
Gnomad4 OTH
AF:
0.578
Alfa
AF:
0.586
Hom.:
11727
Bravo
AF:
0.581
Asia WGS
AF:
0.568
AC:
1974
AN:
3478

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 submitterclinical testingGeneDxNov 11, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.064
DANN
Benign
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2014536; hg19: chr11-117691145; API