chr7-157009949-A-AGCG
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP3BP6_Very_StrongBS1BS2
The NM_005515.4(MNX1):c.401_402insCGC(p.Ala133dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 812,940 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A134A) has been classified as Likely benign.
Frequency
Consequence
NM_005515.4 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MNX1 | NM_005515.4 | c.401_402insCGC | p.Ala133dup | inframe_insertion | 1/3 | ENST00000252971.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MNX1 | ENST00000252971.11 | c.401_402insCGC | p.Ala133dup | inframe_insertion | 1/3 | 1 | NM_005515.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00137 AC: 178AN: 129752Hom.: 2 Cov.: 0
GnomAD4 exome AF: 0.0120 AC: 8194AN: 683180Hom.: 6 Cov.: 28 AF XY: 0.0123 AC XY: 3913AN XY: 319008
GnomAD4 genome AF: 0.00137 AC: 178AN: 129760Hom.: 2 Cov.: 0 AF XY: 0.00127 AC XY: 80AN XY: 62916
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 14, 2015 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at