11-63764871-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144936.2(ZFTA):c.1021C>A(p.Pro341Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,340,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144936.2 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFTA | NM_001144936.2 | c.1021C>A | p.Pro341Thr | missense_variant | 3/5 | ENST00000433688.2 | |
ZFTA | XM_047427478.1 | c.1021C>A | p.Pro341Thr | missense_variant | 3/4 | ||
ZFTA | XM_024448662.2 | c.637+936C>A | intron_variant | ||||
ZFTA | XM_047427477.1 | c.638-273C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFTA | ENST00000433688.2 | c.1021C>A | p.Pro341Thr | missense_variant | 3/5 | 5 | NM_001144936.2 | P1 | |
ZFTA | ENST00000338498.6 | c.156+936C>A | intron_variant | 1 | |||||
ZFTA | ENST00000445014.3 | c.409C>A | p.Pro137Thr | missense_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000373 AC: 5AN: 1340132Hom.: 0 Cov.: 31 AF XY: 0.00000152 AC XY: 1AN XY: 656430
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 25, 2021 | The c.1021C>A (p.P341T) alteration is located in exon 3 (coding exon 3) of the C11orf95 gene. This alteration results from a C to A substitution at nucleotide position 1021, causing the proline (P) at amino acid position 341 to be replaced by a threonine (T). 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