9-137192249-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001128228.3(TPRN):c.2073+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000233 in 1,460,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001128228.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TPRN | ENST00000409012.6 | c.2073+10G>A | intron_variant | Intron 3 of 3 | 1 | NM_001128228.3 | ENSP00000387100.4 | |||
TPRN | ENST00000477345.1 | n.2794+10G>A | intron_variant | Intron 2 of 2 | 1 | |||||
TPRN | ENST00000333046.8 | c.1477G>A | p.Gly493Arg | missense_variant | Exon 3 of 3 | 2 | ENSP00000327617.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250276Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135690
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460828Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726740
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Benign:1
c.2073+10G>A in intron 3 of TPRN: This variant is not expected to have clinical significance because it is not located within the splice consensus sequence. It has been identified in 5/119713 total chromosomes by the Exome Aggregation Cons ortium (ExAC, http://exac.broadinstitute.org; dbSNP rs368771637). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at