rs1042127
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001264.5(CDSN):āc.1222T>Gā(p.Ser408Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,600,850 control chromosomes in the GnomAD database, including 27,576 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001264.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDSN | NM_001264.5 | c.1222T>G | p.Ser408Ala | missense_variant | 2/2 | ENST00000376288.3 | |
PSORS1C1 | NM_014068.3 | c.-229+1502A>C | intron_variant | ENST00000259881.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDSN | ENST00000376288.3 | c.1222T>G | p.Ser408Ala | missense_variant | 2/2 | 1 | NM_001264.5 | P1 | |
PSORS1C1 | ENST00000259881.10 | c.-229+1502A>C | intron_variant | 1 | NM_014068.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.171 AC: 25917AN: 151838Hom.: 2450 Cov.: 31
GnomAD3 exomes AF: 0.208 AC: 46960AN: 226292Hom.: 5284 AF XY: 0.216 AC XY: 26400AN XY: 122090
GnomAD4 exome AF: 0.178 AC: 258103AN: 1448896Hom.: 25131 Cov.: 72 AF XY: 0.185 AC XY: 132863AN XY: 719746
GnomAD4 genome ? AF: 0.170 AC: 25908AN: 151954Hom.: 2445 Cov.: 31 AF XY: 0.176 AC XY: 13099AN XY: 74244
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at