chr14-88479045-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007039.4(PTPN21):āc.2386A>Cā(p.Met796Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,607,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007039.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN21 | NM_007039.4 | c.2386A>C | p.Met796Leu | missense_variant | 13/19 | ENST00000556564.6 | NP_008970.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN21 | ENST00000556564.6 | c.2386A>C | p.Met796Leu | missense_variant | 13/19 | 1 | NM_007039.4 | ENSP00000452414 | P1 | |
PTPN21 | ENST00000328736.7 | c.2386A>C | p.Met796Leu | missense_variant | 12/18 | 1 | ENSP00000330276 | P1 | ||
PTPN21 | ENST00000554270.5 | n.2499A>C | non_coding_transcript_exon_variant | 12/17 | 1 | |||||
PTPN21 | ENST00000536337.5 | c.*2323A>C | 3_prime_UTR_variant, NMD_transcript_variant | 13/19 | 1 | ENSP00000443951 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000696 AC: 17AN: 244400Hom.: 0 AF XY: 0.0000753 AC XY: 10AN XY: 132762
GnomAD4 exome AF: 0.000112 AC: 163AN: 1455142Hom.: 0 Cov.: 30 AF XY: 0.000124 AC XY: 90AN XY: 723674
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2022 | The c.2386A>C (p.M796L) alteration is located in exon 13 (coding exon 12) of the PTPN21 gene. This alteration results from a A to C substitution at nucleotide position 2386, causing the methionine (M) at amino acid position 796 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at