rs41306133
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001008537.3(NEXMIF):āc.2801A>Gā(p.Asn934Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0143 in 1,209,520 control chromosomes in the GnomAD database, including 95 homozygotes. There are 5,511 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001008537.3 missense
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 |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.2801A>G | p.Asn934Ser | missense_variant | 3/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.2801A>G | p.Asn934Ser | missense_variant | 3/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.2801A>G | p.Asn934Ser | missense_variant | 3/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.2801A>G | p.Asn934Ser | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0105 AC: 1169AN: 111819Hom.: 6 Cov.: 23 AF XY: 0.0105 AC XY: 358AN XY: 34015
GnomAD3 exomes AF: 0.0119 AC: 2184AN: 183274Hom.: 10 AF XY: 0.0120 AC XY: 812AN XY: 67790
GnomAD4 exome AF: 0.0147 AC: 16130AN: 1097650Hom.: 88 Cov.: 31 AF XY: 0.0142 AC XY: 5151AN XY: 363038
GnomAD4 genome ? AF: 0.0105 AC: 1177AN: 111870Hom.: 7 Cov.: 23 AF XY: 0.0106 AC XY: 360AN XY: 34076
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 16, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at