chr13-66304858-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_203487.3(PCDH9):c.3511G>A(p.Asp1171Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. D1171H) has been classified as Uncertain significance.
Frequency
Consequence
NM_203487.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151980Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251096Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135722
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461478Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727040
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151980Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74222
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3511G>A (p.D1171N) alteration is located in exon 5 (coding exon 4) of the PCDH9 gene. This alteration results from a G to A substitution at nucleotide position 3511, causing the aspartic acid (D) at amino acid position 1171 to be replaced by an asparagine (N). 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