chrX-74739462-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001008537.3(NEXMIF):c.4494C>T(p.Thr1498=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,197,039 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., 6 hem., cov: 21)
Exomes 𝑓: 0.000012 ( 0 hom. 3 hem. )
Consequence
NEXMIF
NM_001008537.3 synonymous
NM_001008537.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.11
Genes affected
NEXMIF (HGNC:29433): (neurite extension and migration factor) An inversion on the X chromosome which disrupts this gene and a G-protein coupled purinergic receptor gene located in the pseudoautosomal region of the X chromosome has been linked to X linked cognitive disability.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant X-74739462-G-A is Benign according to our data. Variant chrX-74739462-G-A is described in ClinVar as [Benign]. Clinvar id is 2874067.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.11 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 6 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.4494C>T | p.Thr1498= | synonymous_variant | 4/4 | ENST00000055682.12 | NP_001008537.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.4494C>T | p.Thr1498= | synonymous_variant | 4/4 | 1 | NM_001008537.3 | ENSP00000055682 | P1 | |
NEXMIF | ENST00000616200.2 | c.4494C>T | p.Thr1498= | synonymous_variant | 4/5 | 1 | ENSP00000480284 | P1 | ||
NEXMIF | ENST00000642681.2 | c.*634C>T | 3_prime_UTR_variant | 3/3 | ENSP00000495800 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 13AN: 109826Hom.: 0 Cov.: 21 AF XY: 0.000187 AC XY: 6AN XY: 32086
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GnomAD3 exomes AF: 0.0000715 AC: 12AN: 167805Hom.: 0 AF XY: 0.0000362 AC XY: 2AN XY: 55271
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GnomAD4 exome AF: 0.0000120 AC: 13AN: 1087213Hom.: 0 Cov.: 27 AF XY: 0.00000847 AC XY: 3AN XY: 354283
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GnomAD4 genome AF: 0.000118 AC: 13AN: 109826Hom.: 0 Cov.: 21 AF XY: 0.000187 AC XY: 6AN XY: 32086
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 18, 2023 | - - |
NEXMIF-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at