chr16-84850611-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031476.4(CRISPLD2):c.536C>G(p.Thr179Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031476.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRISPLD2 | NM_031476.4 | c.536C>G | p.Thr179Ser | missense_variant | 5/15 | ENST00000262424.10 | |
CRISPLD2 | XM_005256190.2 | c.536C>G | p.Thr179Ser | missense_variant | 6/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRISPLD2 | ENST00000262424.10 | c.536C>G | p.Thr179Ser | missense_variant | 5/15 | 1 | NM_031476.4 | P4 | |
ENST00000648152.1 | n.373-1777G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251490Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135920
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727246
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.536C>G (p.T179S) alteration is located in exon 5 (coding exon 4) of the CRISPLD2 gene. This alteration results from a C to G substitution at nucleotide position 536, causing the threonine (T) at amino acid position 179 to be replaced by a serine (S). 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