chr6-2765656-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020135.3(WRNIP1):c.34C>T(p.Leu12Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000724 in 1,546,874 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 Uncertain significance (★).
Frequency
Consequence
NM_020135.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WRNIP1 | ENST00000380773.9 | c.34C>T | p.Leu12Phe | missense_variant | Exon 1 of 7 | 1 | NM_020135.3 | ENSP00000370150.4 | ||
WRNIP1 | ENST00000618555.4 | c.34C>T | p.Leu12Phe | missense_variant | Exon 1 of 7 | 1 | ENSP00000477551.1 | |||
WRNIP1 | ENST00000380771.8 | c.34C>T | p.Leu12Phe | missense_variant | Exon 1 of 7 | 1 | ENSP00000370148.4 | |||
MYLK4 | ENST00000698899.1 | c.56+4402G>A | intron_variant | Intron 1 of 12 | ENSP00000514016.1 |
Frequencies
GnomAD3 genomes AF: 0.0000594 AC: 9AN: 151616Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000601 AC: 11AN: 183164Hom.: 0 AF XY: 0.0000385 AC XY: 4AN XY: 103858
GnomAD4 exome AF: 0.0000738 AC: 103AN: 1395258Hom.: 0 Cov.: 30 AF XY: 0.0000705 AC XY: 49AN XY: 694668
GnomAD4 genome AF: 0.0000594 AC: 9AN: 151616Hom.: 0 Cov.: 32 AF XY: 0.0000675 AC XY: 5AN XY: 74042
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.34C>T (p.L12F) alteration is located in exon 1 (coding exon 1) of the WRNIP1 gene. This alteration results from a C to T substitution at nucleotide position 34, causing the leucine (L) at amino acid position 12 to be replaced by a phenylalanine (F). 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