rs61740712
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001365276.2(TNXB):c.8601C>T(p.Pro2867Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00982 in 1,613,638 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001365276.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.8601C>T | p.Pro2867Pro | synonymous_variant | Exon 25 of 44 | ENST00000644971.2 | NP_001352205.1 | |
TNXB | NM_001428335.1 | c.9342C>T | p.Pro3114Pro | synonymous_variant | Exon 26 of 45 | NP_001415264.1 | ||
TNXB | NM_019105.8 | c.8595C>T | p.Pro2865Pro | synonymous_variant | Exon 25 of 44 | NP_061978.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.8601C>T | p.Pro2867Pro | synonymous_variant | Exon 25 of 44 | NM_001365276.2 | ENSP00000496448.1 | |||
TNXB | ENST00000647633.1 | c.9342C>T | p.Pro3114Pro | synonymous_variant | Exon 26 of 45 | ENSP00000497649.1 | ||||
TNXB | ENST00000375244.7 | c.8601C>T | p.Pro2867Pro | synonymous_variant | Exon 25 of 44 | 5 | ENSP00000364393.3 |
Frequencies
GnomAD3 genomes AF: 0.00862 AC: 1311AN: 152144Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00859 AC: 2121AN: 246948Hom.: 13 AF XY: 0.00902 AC XY: 1213AN XY: 134438
GnomAD4 exome AF: 0.00995 AC: 14535AN: 1461376Hom.: 79 Cov.: 33 AF XY: 0.0101 AC XY: 7335AN XY: 726982
GnomAD4 genome AF: 0.00860 AC: 1309AN: 152262Hom.: 5 Cov.: 32 AF XY: 0.00884 AC XY: 658AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:2
TNXB: BP4, BP7, BS1, BS2 -
- -
not specified Benign:1
- -
Ehlers-Danlos syndrome Benign:1
- -
Cardiovascular phenotype Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at