NM_002834.5:c.1093-9C>A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_002834.5(PTPN11):c.1093-9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0163 in 1,558,590 control chromosomes in the GnomAD database, including 577 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002834.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN11 | ENST00000351677.7 | c.1093-9C>A | intron_variant | Intron 9 of 15 | 1 | NM_002834.5 | ENSP00000340944.3 | |||
PTPN11 | ENST00000635625.1 | c.1093-9C>A | intron_variant | Intron 9 of 14 | 5 | ENSP00000489597.1 | ||||
PTPN11 | ENST00000635652.1 | c.85-9C>A | intron_variant | Intron 1 of 4 | 3 | ENSP00000489541.1 |
Frequencies
GnomAD3 genomes AF: 0.0390 AC: 5934AN: 152096Hom.: 262 Cov.: 32
GnomAD3 exomes AF: 0.0181 AC: 4555AN: 251222Hom.: 130 AF XY: 0.0160 AC XY: 2177AN XY: 135818
GnomAD4 exome AF: 0.0139 AC: 19496AN: 1406376Hom.: 313 Cov.: 31 AF XY: 0.0134 AC XY: 9417AN XY: 702406
GnomAD4 genome AF: 0.0391 AC: 5952AN: 152214Hom.: 264 Cov.: 32 AF XY: 0.0377 AC XY: 2805AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:8
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Metachondromatosis Benign:2
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:2
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RASopathy Benign:2
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Noonan syndrome 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
LEOPARD syndrome 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Juvenile myelomonocytic leukemia Benign:1
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Noonan syndrome and Noonan-related syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at