chr6-139373408-AGAGCCGCCGGGGGTGCTGCTGCCGCCC-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP5BS2
The NM_006079.5(CITED2):c.510_536del(p.Gly172_Gly180del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000174 in 1,553,684 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. S170S) has been classified as Benign.
Frequency
Consequence
NM_006079.5 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CITED2 | NM_006079.5 | c.510_536del | p.Gly172_Gly180del | inframe_deletion | 2/2 | ENST00000367651.4 | |
CITED2 | NM_001168388.3 | c.510_536del | p.Gly172_Gly180del | inframe_deletion | 2/2 | ||
CITED2 | NM_001168389.3 | c.525_551del | p.Gly177_Gly185del | inframe_deletion | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CITED2 | ENST00000367651.4 | c.510_536del | p.Gly172_Gly180del | inframe_deletion | 2/2 | 1 | NM_006079.5 | P1 | |
ENST00000650173.1 | n.510-55646_510-55620del | intron_variant, non_coding_transcript_variant | |||||||
CITED2 | ENST00000536159.2 | c.510_536del | p.Gly172_Gly180del | inframe_deletion | 2/2 | 3 | P1 | ||
CITED2 | ENST00000537332.2 | c.525_551del | p.Gly177_Gly185del | inframe_deletion | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000180 AC: 27AN: 150200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000142 AC: 27AN: 190406Hom.: 1 AF XY: 0.0000943 AC XY: 10AN XY: 106090
GnomAD4 exome AF: 0.000173 AC: 243AN: 1403372Hom.: 0 AF XY: 0.000176 AC XY: 123AN XY: 697184
GnomAD4 genome ? AF: 0.000180 AC: 27AN: 150312Hom.: 0 Cov.: 32 AF XY: 0.000191 AC XY: 14AN XY: 73438
ClinVar
Submissions by phenotype
Ventricular septal defect 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at