chrX-112455177-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001395362.2(RTL4):c.449C>T(p.Ala150Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000265 in 1,209,646 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 10 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395362.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL4 | NM_001395362.2 | c.449C>T | p.Ala150Val | missense_variant | 5/5 | ENST00000695839.1 | |
RTL4 | NM_001004308.3 | c.449C>T | p.Ala150Val | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL4 | ENST00000695839.1 | c.449C>T | p.Ala150Val | missense_variant | 5/5 | NM_001395362.2 | P1 | ||
RTL4 | ENST00000340433.4 | c.449C>T | p.Ala150Val | missense_variant | 4/4 | P1 | |||
RTL4 | ENST00000695808.1 | c.449C>T | p.Ala150Val | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000161 AC: 18AN: 111583Hom.: 0 Cov.: 23 AF XY: 0.000207 AC XY: 7AN XY: 33759
GnomAD3 exomes AF: 0.0000711 AC: 13AN: 182798Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67554
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1098008Hom.: 0 Cov.: 34 AF XY: 0.00000826 AC XY: 3AN XY: 363388
GnomAD4 genome ? AF: 0.000161 AC: 18AN: 111638Hom.: 0 Cov.: 23 AF XY: 0.000207 AC XY: 7AN XY: 33824
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2023 | The c.449C>T (p.A150V) alteration is located in exon 3 (coding exon 1) of the ZCCHC16 gene. This alteration results from a C to T substitution at nucleotide position 449, causing the alanine (A) at amino acid position 150 to be replaced by a valine (V). 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