chr11-117837222-T-C
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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
NM_022003.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.77
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]
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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 |
---|---|---|---|---|---|---|---|
FXYD6 | NM_022003.4 | c.*1077A>G | 3_prime_UTR_variant | 8/8 | ENST00000526014.6 | ||
FXYD6-FXYD2 | NM_001243598.4 | c.272+2559A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXYD6 | ENST00000526014.6 | c.*1077A>G | 3_prime_UTR_variant | 8/8 | 1 | NM_022003.4 | P1 | ||
FXYD6-AS1 | ENST00000581173.2 | n.386+720T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.535 AC: 81232AN: 151744Hom.: 22357 Cov.: 31
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GnomAD4 exome AF: 0.500 AC: 27AN: 54Hom.: 7 Cov.: 0 AF XY: 0.575 AC XY: 23AN XY: 40
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GnomAD4 genome AF: 0.535 AC: 81295AN: 151860Hom.: 22377 Cov.: 31 AF XY: 0.544 AC XY: 40337AN XY: 74196
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at