chrX-74741756-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001008537.3(NEXMIF):c.2801A>G(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 (★★).
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.2801A>G | p.Asn934Ser | missense_variant | Exon 3 of 4 | 1 | NM_001008537.3 | ENSP00000055682.5 | ||
NEXMIF | ENST00000616200.2 | c.2801A>G | p.Asn934Ser | missense_variant | Exon 3 of 5 | 1 | ENSP00000480284.1 | |||
NEXMIF | ENST00000642681.2 | c.2801A>G | p.Asn934Ser | missense_variant | Exon 3 of 3 | ENSP00000495800.1 |
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:4
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not specified Benign:1
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