Variant rs529623 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000292079.7(FXYD2):c.65-60A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 1,555,572 control chromosomes in the GnomAD database, including 211,077 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.47 ( 17756 hom., cov: 31)

Exomes 𝑓: 0.52 ( 193321 hom. )

Consequence

FXYD2
ENST00000292079.7 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.848

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]

FXYD2 links:

FXYD6-FXYD2 (HGNC:):

FXYD6-FXYD2 links:

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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=-0.86).

BP6

Variant 11-117822540-T-C is Benign according to our data. Variant chr11-117822540-T-C is described in ClinVar as [Benign]. Clinvar id is 1251788.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-117822540-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
FXYD2	NM_001680.5 linkuse as main transcript	c.65-60A>G	intron_variant	ENST00000292079.7	NP_001671.2
FXYD6-FXYD2	NM_001243598.4 linkuse as main transcript	c.311+139A>G	intron_variant		NP_001230527.1
FXYD6-FXYD2	NM_001204268.3 linkuse as main transcript	c.299-60A>G	intron_variant		NP_001191197.1
FXYD2	NM_021603.4 linkuse as main transcript	c.59-60A>G	intron_variant		NP_067614.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FXYD2	ENST00000292079.7 linkuse as main transcript	c.65-60A>G		intron_variant		1	NM_001680.5	ENSP00000292079		P54710-1

Frequencies

GnomAD3 genomes

AF:

0.469

AC:

71139

AN:

151786

Hom.:

17737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.555

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.637

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.474

GnomAD3 exomes

AF:

0.540

AC:

87550

AN:

162008

Hom.:

24129

AF XY:

0.540

AC XY:

46041

AN XY:

85292

show subpopulations

Gnomad AFR exome

AF:

0.286

Gnomad AMR exome

AF:

0.600

Gnomad ASJ exome

AF:

0.560

Gnomad EAS exome

AF:

0.576

Gnomad SAS exome

AF:

0.540

Gnomad FIN exome

AF:

0.632

Gnomad NFE exome

AF:

0.523

Gnomad OTH exome

AF:

0.542

GnomAD4 exome

AF:

0.522

AC:

733219

AN:

1403666

Hom.:

193321

Cov.:

AF XY:

0.523

AC XY:

362279

AN XY:

692530

show subpopulations

Gnomad4 AFR exome

AF:

0.278

Gnomad4 AMR exome

AF:

0.595

Gnomad4 ASJ exome

AF:

0.558

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.544

Gnomad4 FIN exome

AF:

0.634

Gnomad4 NFE exome

AF:

0.520

Gnomad4 OTH exome

AF:

0.518

GnomAD4 genome

AF:

0.469

AC:

71192

AN:

151906

Hom.:

17756

Cov.:

AF XY:

0.475

AC XY:

35284

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.286

Gnomad4 AMR

AF:

0.540

Gnomad4 ASJ

AF:

0.546

Gnomad4 EAS

AF:

0.554

Gnomad4 SAS

AF:

0.551

Gnomad4 FIN

AF:

0.637

Gnomad4 NFE

AF:

0.521

Gnomad4 OTH

AF:

0.478

Alfa

AF:

0.514

Hom.:

31161

Bravo

AF:

0.458

Asia WGS

AF:

0.543

AC:

1887

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 submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 20, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.1

DANN

Benign

0.27

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over