chr7-29512640-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004067.4(CHN2):c.1312C>T(p.Pro438Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,614,034 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_004067.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHN2 | NM_004067.4 | c.1312C>T | p.Pro438Ser | missense_variant | Exon 13 of 13 | ENST00000222792.11 | NP_004058.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0133 AC: 2025AN: 152132Hom.: 57 Cov.: 32
GnomAD3 exomes AF: 0.00375 AC: 942AN: 251260Hom.: 26 AF XY: 0.00281 AC XY: 382AN XY: 135796
GnomAD4 exome AF: 0.00140 AC: 2051AN: 1461786Hom.: 38 Cov.: 31 AF XY: 0.00118 AC XY: 859AN XY: 727202
GnomAD4 genome AF: 0.0133 AC: 2032AN: 152248Hom.: 57 Cov.: 32 AF XY: 0.0131 AC XY: 973AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
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CHN2-related disorder Benign:1
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