19-3543317-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001135580.2(TEKTIP1):c.166C>T(p.Arg56Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000671 in 1,549,316 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001135580.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TEKTIP1 | NM_001135580.2 | c.166C>T | p.Arg56Trp | missense_variant | Exon 2 of 4 | ENST00000329493.6 | NP_001129052.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000165 AC: 25AN: 151914Hom.: 0 AF XY: 0.000111 AC XY: 9AN XY: 81068
GnomAD4 exome AF: 0.0000651 AC: 91AN: 1397036Hom.: 0 Cov.: 31 AF XY: 0.0000551 AC XY: 38AN XY: 689090
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.166C>T (p.R56W) alteration is located in exon 2 (coding exon 2) of the C19orf71 gene. This alteration results from a C to T substitution at nucleotide position 166, causing the arginine (R) at amino acid position 56 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at