rs764439412
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBP6BS2
The NM_001008537.3(NEXMIF):c.2001_2003delAGA(p.Glu667del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000323 in 1,207,812 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001008537.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.2001_2003delAGA | p.Glu667del | disruptive_inframe_deletion | Exon 3 of 4 | 1 | NM_001008537.3 | ENSP00000055682.5 | ||
NEXMIF | ENST00000616200.2 | c.2001_2003delAGA | p.Glu667del | disruptive_inframe_deletion | Exon 3 of 5 | 1 | ENSP00000480284.1 | |||
NEXMIF | ENST00000642681.2 | c.2001_2003delAGA | p.Glu667del | disruptive_inframe_deletion | Exon 3 of 3 | ENSP00000495800.1 |
Frequencies
GnomAD3 genomes AF: 0.0000358 AC: 4AN: 111785Hom.: 0 Cov.: 22 AF XY: 0.0000883 AC XY: 3AN XY: 33971
GnomAD3 exomes AF: 0.0000339 AC: 6AN: 176806Hom.: 0 AF XY: 0.0000321 AC XY: 2AN XY: 62384
GnomAD4 exome AF: 0.0000319 AC: 35AN: 1096027Hom.: 0 AF XY: 0.0000332 AC XY: 12AN XY: 361675
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111785Hom.: 0 Cov.: 22 AF XY: 0.0000883 AC XY: 3AN XY: 33971
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at