18-12817349-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002828.4(PTPN2):c.512C>A(p.Thr171Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,613,352 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002828.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0140 AC: 2136AN: 152112Hom.: 50 Cov.: 32
GnomAD3 exomes AF: 0.00351 AC: 882AN: 251118Hom.: 17 AF XY: 0.00256 AC XY: 347AN XY: 135760
GnomAD4 exome AF: 0.00137 AC: 2002AN: 1461122Hom.: 45 Cov.: 31 AF XY: 0.00114 AC XY: 829AN XY: 726946
GnomAD4 genome AF: 0.0141 AC: 2142AN: 152230Hom.: 50 Cov.: 32 AF XY: 0.0137 AC XY: 1020AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 18, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at