11-63765131-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144936.2(ZFTA):c.761G>A(p.Arg254Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,547,566 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.761G>A | p.Arg254Gln | missense_variant | 3/5 | ENST00000433688.2 | |
ZFTA | XM_047427478.1 | c.761G>A | p.Arg254Gln | missense_variant | 3/4 | ||
ZFTA | XM_024448662.2 | c.637+676G>A | intron_variant | ||||
ZFTA | XM_047427477.1 | c.638-533G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFTA | ENST00000433688.2 | c.761G>A | p.Arg254Gln | missense_variant | 3/5 | 5 | NM_001144936.2 | P1 | |
ZFTA | ENST00000338498.6 | c.156+676G>A | intron_variant | 1 | |||||
ZFTA | ENST00000445014.3 | c.272G>A | p.Arg91Gln | missense_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000129 AC: 18AN: 139546Hom.: 0 AF XY: 0.000106 AC XY: 8AN XY: 75692
GnomAD4 exome AF: 0.000212 AC: 296AN: 1395370Hom.: 0 Cov.: 32 AF XY: 0.000205 AC XY: 141AN XY: 688200
GnomAD4 genome AF: 0.000164 AC: 25AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.761G>A (p.R254Q) alteration is located in exon 3 (coding exon 3) of the C11orf95 gene. This alteration results from a G to A substitution at nucleotide position 761, causing the arginine (R) at amino acid position 254 to be replaced by a glutamine (Q). 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