chr16-67610963-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006565.4(CTCF):āc.131A>Gā(p.Gln44Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000471 in 1,593,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q44K) has been classified as Uncertain significance.
Frequency
Consequence
NM_006565.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTCF | NM_006565.4 | c.131A>G | p.Gln44Arg | missense_variant | 3/12 | ENST00000264010.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTCF | ENST00000264010.10 | c.131A>G | p.Gln44Arg | missense_variant | 3/12 | 1 | NM_006565.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000933 AC: 23AN: 246628Hom.: 0 AF XY: 0.0000451 AC XY: 6AN XY: 133096
GnomAD4 exome AF: 0.0000479 AC: 69AN: 1441344Hom.: 0 Cov.: 31 AF XY: 0.0000421 AC XY: 30AN XY: 712614
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | CTCF: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at