rs118064041
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001079802.2(FKTN):c.1044+44A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 1,509,854 control chromosomes in the GnomAD database, including 904 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 58 hom., cov: 32)
Exomes 𝑓: 0.033 ( 846 hom. )
Consequence
FKTN
NM_001079802.2 intron
NM_001079802.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.363
Genes affected
FKTN (HGNC:3622): (fukutin) The protein encoded by this gene is a putative transmembrane protein that is localized to the cis-Golgi compartment, where it may be involved in the glycosylation of alpha-dystroglycan in skeletal muscle. The encoded protein is thought to be a glycosyltransferase and could play a role in brain development. Defects in this gene are a cause of Fukuyama-type congenital muscular dystrophy (FCMD), Walker-Warburg syndrome (WWS), limb-girdle muscular dystrophy type 2M (LGMD2M), and dilated cardiomyopathy type 1X (CMD1X). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
Variant 9-105618136-A-G is Benign according to our data. Variant chr9-105618136-A-G is described in ClinVar as [Benign]. Clinvar id is 260021.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-105618136-A-G is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0243 (3699/152192) while in subpopulation NFE AF= 0.0385 (2619/67998). AF 95% confidence interval is 0.0373. There are 58 homozygotes in gnomad4. There are 1689 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 58 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKTN | NM_001079802.2 | c.1044+44A>G | intron_variant | ENST00000357998.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKTN | ENST00000357998.10 | c.1044+44A>G | intron_variant | 5 | NM_001079802.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0243 AC: 3698AN: 152074Hom.: 58 Cov.: 32
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GnomAD3 exomes AF: 0.0267 AC: 6635AN: 248588Hom.: 119 AF XY: 0.0271 AC XY: 3663AN XY: 134978
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GnomAD4 exome AF: 0.0332 AC: 45085AN: 1357662Hom.: 846 Cov.: 22 AF XY: 0.0327 AC XY: 22292AN XY: 681274
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GnomAD4 genome ? AF: 0.0243 AC: 3699AN: 152192Hom.: 58 Cov.: 32 AF XY: 0.0227 AC XY: 1689AN XY: 74404
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at