NM_006031.6:c.6876C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_006031.6(PCNT):c.6876C>T(p.Ala2292Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,600,532 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006031.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000519 AC: 12AN: 231288Hom.: 0 AF XY: 0.0000392 AC XY: 5AN XY: 127616
GnomAD4 exome AF: 0.000166 AC: 240AN: 1448318Hom.: 0 Cov.: 34 AF XY: 0.000157 AC XY: 113AN XY: 720822
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74364
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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not specified Benign:1
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PCNT-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at