chr2-1649050-T-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP7BS1
The NM_012293.3(PXDN):c.2730A>T(p.Ile910=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,612,630 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. I910I) has been classified as Benign.
Frequency
Consequence
NM_012293.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.2730A>T | p.Ile910= | synonymous_variant | 17/23 | ENST00000252804.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.2730A>T | p.Ile910= | synonymous_variant | 17/23 | 1 | NM_012293.3 | P1 | |
PXDN | ENST00000478155.5 | n.2697-4298A>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000409 AC: 10AN: 244392Hom.: 0 AF XY: 0.0000374 AC XY: 5AN XY: 133736
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1460472Hom.: 0 Cov.: 99 AF XY: 0.0000151 AC XY: 11AN XY: 726548
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74380
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at