5-141151296-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018939.4(PCDHB6):c.1039A>T(p.Met347Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000317 in 1,614,086 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018939.4 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 |
---|---|---|---|---|---|---|---|
PCDHB6 | NM_018939.4 | c.1039A>T | p.Met347Leu | missense_variant | 1/1 | ENST00000231136.4 | |
PCDHB6 | NM_001303145.2 | c.631A>T | p.Met211Leu | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHB6 | ENST00000231136.4 | c.1039A>T | p.Met347Leu | missense_variant | 1/1 | NM_018939.4 | P1 | ||
ENST00000624192.1 | n.73-14113T>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000624802.1 | n.364+21137T>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000290 AC: 73AN: 251484Hom.: 1 AF XY: 0.000280 AC XY: 38AN XY: 135918
GnomAD4 exome AF: 0.000324 AC: 473AN: 1461894Hom.: 1 Cov.: 87 AF XY: 0.000305 AC XY: 222AN XY: 727248
GnomAD4 genome AF: 0.000256 AC: 39AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74402
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.1039A>T (p.M347L) alteration is located in exon 1 (coding exon 1) of the PCDHB6 gene. This alteration results from a A to T substitution at nucleotide position 1039, causing the methionine (M) at amino acid position 347 to be replaced by a leucine (L). 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