chr7-110886666-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_032549.4(IMMP2L):c.335A>G(p.Lys112Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00072 in 1,603,170 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_032549.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IMMP2L | NM_032549.4 | c.335A>G | p.Lys112Arg | missense_variant | 5/6 | ENST00000405709.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMMP2L | ENST00000405709.7 | c.335A>G | p.Lys112Arg | missense_variant | 5/6 | 1 | NM_032549.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000434 AC: 66AN: 152108Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00142 AC: 355AN: 250594Hom.: 1 AF XY: 0.00184 AC XY: 249AN XY: 135486
GnomAD4 exome AF: 0.000752 AC: 1091AN: 1450946Hom.: 10 Cov.: 26 AF XY: 0.00103 AC XY: 746AN XY: 722678
GnomAD4 genome ? AF: 0.000420 AC: 64AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.000524 AC XY: 39AN XY: 74416
ClinVar
Submissions by phenotype
IMMP2L-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 27, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at