chr1-43442603-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001365999.1(SZT2):c.8136C>T(p.Pro2712Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,604,230 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001365999.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SZT2 | ENST00000634258.3 | c.8136C>T | p.Pro2712Pro | synonymous_variant | Exon 58 of 72 | 5 | NM_001365999.1 | ENSP00000489255.1 | ||
SZT2 | ENST00000562955.2 | c.7965C>T | p.Pro2655Pro | synonymous_variant | Exon 57 of 71 | 5 | ENSP00000457168.1 | |||
SZT2 | ENST00000648058.1 | n.4590C>T | non_coding_transcript_exon_variant | Exon 26 of 40 | ||||||
SZT2 | ENST00000649403.1 | n.2886C>T | non_coding_transcript_exon_variant | Exon 23 of 37 |
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 230AN: 152176Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00367 AC: 906AN: 246552Hom.: 18 AF XY: 0.00351 AC XY: 467AN XY: 133194
GnomAD4 exome AF: 0.00103 AC: 1490AN: 1451936Hom.: 18 Cov.: 36 AF XY: 0.00103 AC XY: 740AN XY: 720628
GnomAD4 genome AF: 0.00150 AC: 229AN: 152294Hom.: 9 Cov.: 32 AF XY: 0.00184 AC XY: 137AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:2
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Developmental and epileptic encephalopathy, 18 Benign:1
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not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at