chr6-63550374-A-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000701584.1(ENSG00000289911):n.133+15724T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,952 control chromosomes in the GnomAD database, including 5,746 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTP4A1 | NM_001385255.1 | c.-565A>C | 5_prime_UTR_variant | 4/9 | |||
PTP4A1 | NM_001385257.1 | c.-565A>C | 5_prime_UTR_variant | 4/9 | |||
PTP4A1 | NM_001385258.1 | c.-565A>C | 5_prime_UTR_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000701584.1 | n.133+15724T>G | intron_variant, non_coding_transcript_variant | |||||||
PTP4A1 | ENST00000639568.2 | c.-565A>C | 5_prime_UTR_variant | 3/4 | 5 | ||||
PTP4A1 | ENST00000648894.1 | c.-446+17844A>C | intron_variant | P1 | |||||
PTP4A1 | ENST00000470661.1 | n.332+22290A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.253 AC: 38469AN: 151834Hom.: 5739 Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 6Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
GnomAD4 genome AF: 0.253 AC: 38475AN: 151952Hom.: 5746 Cov.: 31 AF XY: 0.253 AC XY: 18782AN XY: 74272
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at