10-119157933-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_213649.2(SFXN4):c.415-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 1,613,640 control chromosomes in the GnomAD database, including 203,917 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_213649.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SFXN4 | NM_213649.2 | c.415-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000355697.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SFXN4 | ENST00000355697.7 | c.415-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_213649.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.484 AC: 73617AN: 152032Hom.: 18089 Cov.: 34
GnomAD3 exomes AF: 0.499 AC: 125461AN: 251420Hom.: 32045 AF XY: 0.497 AC XY: 67553AN XY: 135878
GnomAD4 exome AF: 0.502 AC: 733778AN: 1461490Hom.: 185812 Cov.: 50 AF XY: 0.500 AC XY: 363626AN XY: 727064
GnomAD4 genome AF: 0.484 AC: 73672AN: 152150Hom.: 18105 Cov.: 34 AF XY: 0.482 AC XY: 35863AN XY: 74386
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 19, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 02, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at