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GeneBe

11-117837222-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022003.4(FXYD6):​c.*1077A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,914 control chromosomes in the GnomAD database, including 22,384 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22377 hom., cov: 31)
Exomes 𝑓: 0.50 ( 7 hom. )

Consequence

FXYD6
NM_022003.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.77
Variant links:
Genes affected
FXYD6 (HGNC:4030): (FXYD domain containing ion transport regulator 6) This gene encodes a member of the FXYD family of transmembrane proteins. This particular protein encodes phosphohippolin, which likely affects the activity of Na,K-ATPase. Multiple alternatively spliced transcript variants encoding the same protein have been described. Related pseudogenes have been identified on chromosomes 10 and X. Read-through transcripts have been observed between this locus and the downstream sodium/potassium-transporting ATPase subunit gamma (FXYD2, GeneID 486) locus.[provided by RefSeq, Feb 2011]
FXYD6-AS1 (HGNC:56067): (FXYD6 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FXYD6NM_022003.4 linkuse as main transcriptc.*1077A>G 3_prime_UTR_variant 8/8 ENST00000526014.6
FXYD6-FXYD2NM_001243598.4 linkuse as main transcriptc.272+2559A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FXYD6ENST00000526014.6 linkuse as main transcriptc.*1077A>G 3_prime_UTR_variant 8/81 NM_022003.4 P1Q9H0Q3-1
FXYD6-AS1ENST00000581173.2 linkuse as main transcriptn.386+720T>C intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.535
AC:
81232
AN:
151744
Hom.:
22357
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.599
Gnomad AMI
AF:
0.365
Gnomad AMR
AF:
0.582
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.727
Gnomad SAS
AF:
0.612
Gnomad FIN
AF:
0.589
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.470
Gnomad OTH
AF:
0.462
GnomAD4 exome
AF:
0.500
AC:
27
AN:
54
Hom.:
7
Cov.:
0
AF XY:
0.575
AC XY:
23
AN XY:
40
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.500
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.475
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.535
AC:
81295
AN:
151860
Hom.:
22377
Cov.:
31
AF XY:
0.544
AC XY:
40337
AN XY:
74196
show subpopulations
Gnomad4 AFR
AF:
0.599
Gnomad4 AMR
AF:
0.583
Gnomad4 ASJ
AF:
0.393
Gnomad4 EAS
AF:
0.728
Gnomad4 SAS
AF:
0.613
Gnomad4 FIN
AF:
0.589
Gnomad4 NFE
AF:
0.470
Gnomad4 OTH
AF:
0.455
Alfa
AF:
0.479
Hom.:
25220
Bravo
AF:
0.540
Asia WGS
AF:
0.637
AC:
2215
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.018
DANN
Benign
0.48

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs3087563; hg19: chr11-117707937; API