10-119140986-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_213649.2(SFXN4):c.*256G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 392,108 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00048 ( 0 hom. )
Consequence
SFXN4
NM_213649.2 3_prime_UTR
NM_213649.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.60
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 10-119140986-C-T is Benign according to our data. Variant chr10-119140986-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1186555.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00308 (468/152184) while in subpopulation AFR AF= 0.0107 (445/41504). AF 95% confidence interval is 0.0099. There are 2 homozygotes in gnomad4. There are 234 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFXN4 | NM_213649.2 | c.*256G>A | 3_prime_UTR_variant | 14/14 | ENST00000355697.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFXN4 | ENST00000355697.7 | c.*256G>A | 3_prime_UTR_variant | 14/14 | 1 | NM_213649.2 | P1 | ||
SFXN4 | ENST00000484960.5 | n.482G>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
SFXN4 | ENST00000490417.6 | n.733G>A | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00306 AC: 466AN: 152066Hom.: 2 Cov.: 32
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GnomAD4 exome AF: 0.000475 AC: 114AN: 239924Hom.: 0 Cov.: 0 AF XY: 0.000421 AC XY: 52AN XY: 123544
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GnomAD4 genome AF: 0.00308 AC: 468AN: 152184Hom.: 2 Cov.: 32 AF XY: 0.00314 AC XY: 234AN XY: 74418
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 17, 2018 | - - |
Computational scores
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at