5-141199880-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018931.3(PCDHB11):c.106G>A(p.Ala36Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018931.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHB11 | NM_018931.3 | c.106G>A | p.Ala36Thr | missense_variant | 1/1 | ENST00000354757.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHB11 | ENST00000354757.5 | c.106G>A | p.Ala36Thr | missense_variant | 1/1 | NM_018931.3 | P1 | ||
ENST00000624192.1 | n.72+41793C>T | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000624549.1 | n.131+1386C>T | intron_variant, non_coding_transcript_variant | 4 | ||||||
PCDHB11 | ENST00000624887.1 | c.-364+71G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251492Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135922
GnomAD4 exome AF: 0.000103 AC: 151AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.0000949 AC XY: 69AN XY: 727248
GnomAD4 genome AF: 0.000112 AC: 17AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74334
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at