chr11-117820548-C-A

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

Scores

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.317
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]

Genome browser will be placed here

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
FXYD2NM_001680.5 linkuse as main transcriptc.*6+118G>T intron_variant ENST00000292079.7
FXYD6-FXYD2NM_001243598.4 linkuse as main transcriptc.*40+118G>T intron_variant
FXYD6-FXYD2NM_001204268.3 linkuse as main transcriptc.*6+118G>T intron_variant
FXYD2NM_021603.4 linkuse as main transcriptc.*6+118G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FXYD2ENST00000292079.7 linkuse as main transcriptc.*6+118G>T intron_variant 1 NM_001680.5 P54710-1
ENST00000531850.2 linkuse as main transcriptn.364C>A non_coding_transcript_exon_variant 2/35

Frequencies

GnomAD3 genomes
AF:
0.0147
AC:
2230
AN:
152202
Hom.:
32
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0370
Gnomad AMI
AF:
0.00329
Gnomad AMR
AF:
0.0155
Gnomad ASJ
AF:
0.00864
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.00476
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.0285
Gnomad NFE
AF:
0.00504
Gnomad OTH
AF:
0.0224
GnomAD4 exome
AF:
0.00567
AC:
6508
AN:
1148196
Hom.:
66
Cov.:
15
AF XY:
0.00577
AC XY:
3336
AN XY:
577774
show subpopulations
Gnomad4 AFR exome
AF:
0.0393
Gnomad4 AMR exome
AF:
0.00776
Gnomad4 ASJ exome
AF:
0.0110
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00672
Gnomad4 FIN exome
AF:
0.000380
Gnomad4 NFE exome
AF:
0.00437
Gnomad4 OTH exome
AF:
0.00972
GnomAD4 genome
AF:
0.0147
AC:
2234
AN:
152320
Hom.:
32
Cov.:
32
AF XY:
0.0144
AC XY:
1072
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0370
Gnomad4 AMR
AF:
0.0156
Gnomad4 ASJ
AF:
0.00864
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.00477
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.00504
Gnomad4 OTH
AF:
0.0222
Alfa
AF:
0.0134
Hom.:
2
Bravo
AF:
0.0170
Asia WGS
AF:
0.00433
AC:
15
AN:
3478

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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Likely benign, criteria provided, single submitterclinical testingGeneDxNov 08, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
7.1
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.23
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.23
Position offset: -5

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: rs114805473; hg19: chr11-117691263; API