chr5-151049891-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006058.5(TNIP1):c.779C>T(p.Ala260Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00496 in 1,614,088 control chromosomes in the GnomAD database, including 201 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006058.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNIP1 | NM_006058.5 | c.779C>T | p.Ala260Val | missense_variant | 8/18 | ENST00000521591.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNIP1 | ENST00000521591.6 | c.779C>T | p.Ala260Val | missense_variant | 8/18 | 1 | NM_006058.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0207 AC: 3152AN: 152132Hom.: 96 Cov.: 32
GnomAD3 exomes AF: 0.00740 AC: 1860AN: 251400Hom.: 45 AF XY: 0.00605 AC XY: 822AN XY: 135866
GnomAD4 exome AF: 0.00331 AC: 4845AN: 1461838Hom.: 102 Cov.: 30 AF XY: 0.00309 AC XY: 2248AN XY: 727224
GnomAD4 genome ? AF: 0.0208 AC: 3166AN: 152250Hom.: 99 Cov.: 32 AF XY: 0.0206 AC XY: 1532AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at