chr8-2942602-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_033225.6(CSMD1):c.10405C>G(p.Pro3469Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,567,484 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_033225.6 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSMD1 | NM_033225.6 | c.10405C>G | p.Pro3469Ala | missense_variant, splice_region_variant | 69/70 | ENST00000635120.2 | |
LOC105377785 | NR_168443.1 | n.1172-65966G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSMD1 | ENST00000635120.2 | c.10405C>G | p.Pro3469Ala | missense_variant, splice_region_variant | 69/70 | 5 | NM_033225.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000808 AC: 123AN: 152178Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00313 AC: 575AN: 183730Hom.: 15 AF XY: 0.00407 AC XY: 400AN XY: 98264
GnomAD4 exome AF: 0.00135 AC: 1911AN: 1415188Hom.: 40 Cov.: 30 AF XY: 0.00196 AC XY: 1372AN XY: 700220
GnomAD4 genome ? AF: 0.000808 AC: 123AN: 152296Hom.: 5 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74478
ClinVar
Submissions by phenotype
CSMD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 20, 2021 | 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