rs202209156
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4BP6BS1BS2
The NM_000751.3(CHRND):c.817G>A(p.Asp273Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000224 in 1,614,020 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000751.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRND | NM_000751.3 | c.817G>A | p.Asp273Asn | missense_variant | Exon 7 of 12 | ENST00000258385.8 | NP_000742.1 | |
CHRND | NM_001256657.2 | c.772G>A | p.Asp258Asn | missense_variant | Exon 6 of 11 | NP_001243586.1 | ||
CHRND | NM_001311196.2 | c.514G>A | p.Asp172Asn | missense_variant | Exon 7 of 12 | NP_001298125.1 | ||
CHRND | NM_001311195.2 | c.239-1216G>A | intron_variant | Intron 5 of 9 | NP_001298124.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000267 AC: 67AN: 250804Hom.: 1 AF XY: 0.000243 AC XY: 33AN XY: 135614
GnomAD4 exome AF: 0.000196 AC: 287AN: 1461766Hom.: 2 Cov.: 32 AF XY: 0.000202 AC XY: 147AN XY: 727178
GnomAD4 genome AF: 0.000486 AC: 74AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.000484 AC XY: 36AN XY: 74442
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
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This variant is associated with the following publications: (PMID: 28518170) -
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Lethal multiple pterygium syndrome Benign:1
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CHRND-related disorder Benign:1
This variant is classified as likely 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