6-139373363-G-A
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006079.5(CITED2):c.582C>T(p.Gly194Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00373 in 1,582,560 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006079.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CITED2 | NM_006079.5 | c.582C>T | p.Gly194Gly | synonymous_variant | Exon 2 of 2 | ENST00000367651.4 | NP_006070.2 | |
CITED2 | NM_001168389.3 | c.597C>T | p.Gly199Gly | synonymous_variant | Exon 2 of 2 | NP_001161861.2 | ||
CITED2 | NM_001168388.3 | c.582C>T | p.Gly194Gly | synonymous_variant | Exon 2 of 2 | NP_001161860.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CITED2 | ENST00000367651.4 | c.582C>T | p.Gly194Gly | synonymous_variant | Exon 2 of 2 | 1 | NM_006079.5 | ENSP00000356623.2 | ||
CITED2 | ENST00000537332.2 | c.597C>T | p.Gly199Gly | synonymous_variant | Exon 2 of 2 | 3 | ENSP00000444198.2 | |||
CITED2 | ENST00000536159.2 | c.582C>T | p.Gly194Gly | synonymous_variant | Exon 2 of 2 | 3 | ENSP00000442831.1 | |||
ENSG00000226571 | ENST00000650173.1 | n.510-55718G>A | intron_variant | Intron 4 of 7 |
Frequencies
GnomAD3 genomes AF: 0.00242 AC: 367AN: 151580Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00221 AC: 473AN: 214128Hom.: 1 AF XY: 0.00208 AC XY: 249AN XY: 119770
GnomAD4 exome AF: 0.00387 AC: 5536AN: 1430872Hom.: 14 Cov.: 31 AF XY: 0.00379 AC XY: 2701AN XY: 712070
GnomAD4 genome AF: 0.00242 AC: 367AN: 151688Hom.: 2 Cov.: 32 AF XY: 0.00237 AC XY: 176AN XY: 74198
ClinVar
Submissions by phenotype
not provided Benign:2
CITED2: BP4, BP7, BS2 -
- -
CITED2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at