chr20-35672958-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_021100.5(NFS1):c.1221-114A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00366 in 659,448 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 21 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 15 hom. )
Consequence
NFS1
NM_021100.5 intron
NM_021100.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.644
Genes affected
NFS1 (HGNC:15910): (NFS1 cysteine desulfurase) Iron-sulfur clusters are required for the function of many cellular enzymes. The proteins encoded by this gene supply inorganic sulfur to these clusters by removing the sulfur from cysteine, creating alanine in the process. This gene uses alternate in-frame translation initiation sites to generate mitochondrial forms and cytoplasmic/nuclear forms. Selection of the alternative initiation sites is determined by the cytosolic pH. The encoded proteins belong to the class-V family of pyridoxal phosphate-dependent aminotransferases. Alternatively spliced transcript variants have been described. [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=-0.88).
BP6
?
Variant 20-35672958-T-A is Benign according to our data. Variant chr20-35672958-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316339.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0104 (1587/152230) while in subpopulation AFR AF= 0.0352 (1462/41542). AF 95% confidence interval is 0.0337. There are 21 homozygotes in gnomad4. There are 745 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 21 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NFS1 | NM_021100.5 | c.1221-114A>T | intron_variant | ENST00000374092.9 | |||
NFS1 | NM_001198989.2 | c.1068-114A>T | intron_variant | ||||
NFS1 | NR_037570.3 | n.1407-114A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NFS1 | ENST00000374092.9 | c.1221-114A>T | intron_variant | 1 | NM_021100.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1583AN: 152112Hom.: 21 Cov.: 32
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GnomAD4 exome AF: 0.00162 AC: 824AN: 507218Hom.: 15 AF XY: 0.00136 AC XY: 366AN XY: 268310
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GnomAD4 genome ? AF: 0.0104 AC: 1587AN: 152230Hom.: 21 Cov.: 32 AF XY: 0.0100 AC XY: 745AN XY: 74438
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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 | Jul 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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