chr1-11847311-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_006172.4(NPPA):āc.252C>Gā(p.Thr84=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T84T) has been classified as Likely benign.
Frequency
Consequence
NM_006172.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPPA | NM_006172.4 | c.252C>G | p.Thr84= | synonymous_variant | 2/3 | ENST00000376480.7 | |
NPPA-AS1 | NR_037806.1 | n.1480-123G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPPA | ENST00000376480.7 | c.252C>G | p.Thr84= | synonymous_variant | 2/3 | 1 | NM_006172.4 | P1 | |
CLCN6 | ENST00000446542.5 | n.782-123G>C | intron_variant, non_coding_transcript_variant | 1 | |||||
NPPA | ENST00000376476.1 | c.102C>G | p.Thr34= | synonymous_variant | 2/3 | 3 | |||
CLCN6 | ENST00000400892.3 | c.*1962-266G>C | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461140Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726804
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at