chrX-74739463-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001008537.3(NEXMIF):c.4493C>A(p.Thr1498Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000376 in 1,197,541 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001008537.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.4493C>A | p.Thr1498Asn | missense_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.4493C>A | p.Thr1498Asn | missense_variant | 4/4 | 1 | NM_001008537.3 | ENSP00000055682 | P1 | |
NEXMIF | ENST00000616200.2 | c.4493C>A | p.Thr1498Asn | missense_variant | 4/5 | 1 | ENSP00000480284 | P1 | ||
NEXMIF | ENST00000642681.2 | c.*633C>A | 3_prime_UTR_variant | 3/3 | ENSP00000495800 |
Frequencies
GnomAD3 genomes AF: 0.0000182 AC: 2AN: 109722Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32016
GnomAD3 exomes AF: 0.0000357 AC: 6AN: 168121Hom.: 0 AF XY: 0.0000721 AC XY: 4AN XY: 55481
GnomAD4 exome AF: 0.0000395 AC: 43AN: 1087819Hom.: 0 Cov.: 27 AF XY: 0.0000451 AC XY: 16AN XY: 354749
GnomAD4 genome AF: 0.0000182 AC: 2AN: 109722Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32016
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2018 | This alteration is classified as likely 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at