chr5-141122851-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_018938.4(PCDHB4):c.853G>C(p.Asp285His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00593 in 1,613,980 control chromosomes in the GnomAD database, including 145 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_018938.4 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 |
---|---|---|---|---|---|---|---|
PCDHB4 | NM_018938.4 | c.853G>C | p.Asp285His | missense_variant | 1/1 | ENST00000194152.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHB4 | ENST00000194152.4 | c.853G>C | p.Asp285His | missense_variant | 1/1 | NM_018938.4 | P1 | ||
ENST00000624802.1 | n.365-22096C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00425 AC: 646AN: 152140Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00809 AC: 2028AN: 250542Hom.: 36 AF XY: 0.0102 AC XY: 1390AN XY: 135778
GnomAD4 exome AF: 0.00611 AC: 8931AN: 1461722Hom.: 141 Cov.: 34 AF XY: 0.00732 AC XY: 5322AN XY: 727156
GnomAD4 genome ? AF: 0.00424 AC: 646AN: 152258Hom.: 4 Cov.: 32 AF XY: 0.00471 AC XY: 351AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at