rs148005156
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001008537.3(NEXMIF):c.1716G>T(p.Glu572Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000043 in 1,209,388 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. E572E) has been classified as Likely benign.
Frequency
Consequence
NM_001008537.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.1716G>T | p.Glu572Asp | missense_variant | 3/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.1716G>T | p.Glu572Asp | missense_variant | 3/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.1716G>T | p.Glu572Asp | missense_variant | 3/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.1716G>T | p.Glu572Asp | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.000278 AC: 31AN: 111378Hom.: 0 Cov.: 22 AF XY: 0.000358 AC XY: 12AN XY: 33566
GnomAD3 exomes AF: 0.0000656 AC: 12AN: 183015Hom.: 0 AF XY: 0.0000444 AC XY: 3AN XY: 67581
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1097955Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 6AN XY: 363319
GnomAD4 genome ? AF: 0.000278 AC: 31AN: 111433Hom.: 0 Cov.: 22 AF XY: 0.000357 AC XY: 12AN XY: 33631
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2019 | The p.E572D variant (also known as c.1716G>T), located in coding exon 2 of the KIAA2022 gene, results from a G to T substitution at nucleotide position 1716. The glutamic acid at codon 572 is replaced by aspartic acid, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at