X-74739489-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001008537.3(NEXMIF):c.4467C>T(p.Asp1489=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000169 in 1,186,410 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000092 ( 0 hom., 0 hem., cov: 21)
Exomes 𝑓: 9.3e-7 ( 0 hom. 0 hem. )
Consequence
NEXMIF
NM_001008537.3 synonymous
NM_001008537.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.79
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant X-74739489-G-A is Benign according to our data. Variant chrX-74739489-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1130192.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.4467C>T | p.Asp1489= | synonymous_variant | 4/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.4467C>T | p.Asp1489= | synonymous_variant | 4/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.4467C>T | p.Asp1489= | synonymous_variant | 4/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.*607C>T | 3_prime_UTR_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.00000916 AC: 1AN: 109111Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 31383
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GnomAD3 exomes AF: 0.0000120 AC: 2AN: 166812Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 53910
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GnomAD4 exome AF: 9.28e-7 AC: 1AN: 1077299Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 344437
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GnomAD4 genome AF: 0.00000916 AC: 1AN: 109111Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 31383
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Computational scores
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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