6-31116174-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001264.5(CDSN):c.1441G>A(p.Ala481Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,612,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A481S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001264.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDSN | NM_001264.5 | c.1441G>A | p.Ala481Thr | missense_variant | 2/2 | ENST00000376288.3 | |
PSORS1C1 | NM_014068.3 | c.-229+1283C>T | intron_variant | ENST00000259881.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDSN | ENST00000376288.3 | c.1441G>A | p.Ala481Thr | missense_variant | 2/2 | 1 | NM_001264.5 | P1 | |
PSORS1C1 | ENST00000259881.10 | c.-229+1283C>T | intron_variant | 1 | NM_014068.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000211 AC: 32AN: 151992Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000809 AC: 20AN: 247144Hom.: 0 AF XY: 0.0000745 AC XY: 10AN XY: 134302
GnomAD4 exome AF: 0.0000466 AC: 68AN: 1460074Hom.: 0 Cov.: 58 AF XY: 0.0000317 AC XY: 23AN XY: 726090
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152110Hom.: 0 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74358
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2022 | The c.1441G>A (p.A481T) alteration is located in exon 2 (coding exon 2) of the CDSN gene. This alteration results from a G to A substitution at nucleotide position 1441, causing the alanine (A) at amino acid position 481 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at