rs377223489
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002831.6(PTPN6):c.9-7C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_002831.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151902Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249242Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135340
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461766Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727172
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151902Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74200
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at