chr11-117820637-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.*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

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.158
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=-0.88).
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
FXYD2NM_001680.5 linkuse as main transcriptc.*6+29G>A intron_variant ENST00000292079.7
FXYD6-FXYD2NM_001243598.4 linkuse as main transcriptc.*40+29G>A intron_variant
FXYD6-FXYD2NM_001204268.3 linkuse as main transcriptc.*6+29G>A intron_variant
FXYD2NM_021603.4 linkuse as main transcriptc.*6+29G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FXYD2ENST00000292079.7 linkuse as main transcriptc.*6+29G>A intron_variant 1 NM_001680.5 P54710-1
ENST00000531850.2 linkuse as main transcriptn.453C>T non_coding_transcript_exon_variant 2/35

Frequencies

GnomAD3 genomes
AF:
0.00224
AC:
341
AN:
152154
Hom.:
12
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0575
Gnomad SAS
AF:
0.00394
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00447
AC:
1120
AN:
250342
Hom.:
32
AF XY:
0.00407
AC XY:
551
AN XY:
135386
show subpopulations
Gnomad AFR exome
AF:
0.000370
Gnomad AMR exome
AF:
0.000174
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0578
Gnomad SAS exome
AF:
0.00114
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.00164
GnomAD4 exome
AF:
0.00156
AC:
2273
AN:
1461184
Hom.:
52
Cov.:
31
AF XY:
0.00151
AC XY:
1096
AN XY:
726940
show subpopulations
Gnomad4 AFR exome
AF:
0.000149
Gnomad4 AMR exome
AF:
0.000201
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0472
Gnomad4 SAS exome
AF:
0.00136
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000342
Gnomad4 OTH exome
AF:
0.00383
GnomAD4 genome
AF:
0.00223
AC:
339
AN:
152272
Hom.:
11
Cov.:
32
AF XY:
0.00239
AC XY:
178
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.000719
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0573
Gnomad4 SAS
AF:
0.00394
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00114
Hom.:
1
Bravo
AF:
0.00244
Asia WGS
AF:
0.0260
AC:
90
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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 24, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
3.7
DANN
Benign
0.59
RBP_binding_hub_radar
0.97
RBP_regulation_power_radar
2.3

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: rs118032332; hg19: chr11-117691352; API