rs201351157
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001008537.3(NEXMIF):c.206C>T(p.Ser69Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,209,734 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001008537.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.206C>T | p.Ser69Phe | missense_variant | 3/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.206C>T | p.Ser69Phe | missense_variant | 3/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.206C>T | p.Ser69Phe | missense_variant | 3/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.206C>T | p.Ser69Phe | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.000134 AC: 15AN: 111677Hom.: 0 Cov.: 22 AF XY: 0.0000591 AC XY: 2AN XY: 33847
GnomAD3 exomes AF: 0.0000877 AC: 16AN: 182346Hom.: 0 AF XY: 0.0000745 AC XY: 5AN XY: 67092
GnomAD4 exome AF: 0.000132 AC: 145AN: 1098002Hom.: 0 Cov.: 32 AF XY: 0.000105 AC XY: 38AN XY: 363378
GnomAD4 genome ? AF: 0.000134 AC: 15AN: 111732Hom.: 0 Cov.: 22 AF XY: 0.0000590 AC XY: 2AN XY: 33912
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 17, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 24, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 20, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at