rs2275112
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_213649.2(SFXN4):c.361-42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,589,208 control chromosomes in the GnomAD database, including 98,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.30 ( 7566 hom., cov: 32)
Exomes 𝑓: 0.35 ( 90593 hom. )
Consequence
SFXN4
NM_213649.2 intron
NM_213649.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0650
Genes affected
SFXN4 (HGNC:16088): (sideroflexin 4) This gene encodes a member of the sideroflexin family. The encoded protein is a transmembrane protein of the inner mitochondrial membrane, and is required for mitochondrial respiratory homeostasis and erythropoiesis. Mutations in this gene are associated with mitochondriopathy and macrocytic anemia. Alternatively spliced transcript variants have been found in this gene. [provided by RefSeq, Jan 2014]
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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=-0.81).
BP6
?
Variant 10-119158104-G-A is Benign according to our data. Variant chr10-119158104-G-A is described in ClinVar as [Benign]. Clinvar id is 1292078.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFXN4 | NM_213649.2 | c.361-42C>T | intron_variant | ENST00000355697.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFXN4 | ENST00000355697.7 | c.361-42C>T | intron_variant | 1 | NM_213649.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.299 AC: 45456AN: 151926Hom.: 7569 Cov.: 32
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GnomAD3 exomes AF: 0.332 AC: 83235AN: 251032Hom.: 14641 AF XY: 0.340 AC XY: 46150AN XY: 135782
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GnomAD4 exome AF: 0.351 AC: 504415AN: 1437162Hom.: 90593 Cov.: 26 AF XY: 0.353 AC XY: 253143AN XY: 716510
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GnomAD4 genome ? AF: 0.299 AC: 45453AN: 152046Hom.: 7566 Cov.: 32 AF XY: 0.304 AC XY: 22587AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Growth and developmental delay-hypotonia-vision impairment-lactic acidosis syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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