chr8-2942574-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_033225.6(CSMD1):c.10433G>A(p.Ser3478Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0236 in 1,600,802 control chromosomes in the GnomAD database, including 1,292 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_033225.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSMD1 | NM_033225.6 | c.10433G>A | p.Ser3478Asn | missense_variant | 69/70 | ENST00000635120.2 | |
LOC105377785 | NR_168443.1 | n.1172-65994C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSMD1 | ENST00000635120.2 | c.10433G>A | p.Ser3478Asn | missense_variant | 69/70 | 5 | NM_033225.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0560 AC: 8523AN: 152074Hom.: 556 Cov.: 32
GnomAD3 exomes AF: 0.0265 AC: 5979AN: 225504Hom.: 240 AF XY: 0.0252 AC XY: 3060AN XY: 121590
GnomAD4 exome AF: 0.0202 AC: 29248AN: 1448610Hom.: 731 Cov.: 30 AF XY: 0.0202 AC XY: 14520AN XY: 719072
GnomAD4 genome ? AF: 0.0562 AC: 8556AN: 152192Hom.: 561 Cov.: 32 AF XY: 0.0545 AC XY: 4058AN XY: 74450
ClinVar
Submissions by phenotype
CSMD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 05, 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