9-32459452-T-G
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_014314.4(RIGI):c.2400A>C(p.Val800Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,612,956 control chromosomes in the GnomAD database, including 98,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_014314.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- Singleton-Merten syndrome 2Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- Singleton-Merten dysplasiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIGI | ENST00000379883.3 | c.2400A>C | p.Val800Val | synonymous_variant | Exon 17 of 18 | 1 | NM_014314.4 | ENSP00000369213.2 | ||
ENSG00000288684 | ENST00000681750.1 | c.2250A>C | p.Val750Val | synonymous_variant | Exon 19 of 20 | ENSP00000506413.1 |
Frequencies
GnomAD3 genomes AF: 0.325 AC: 49411AN: 151928Hom.: 8345 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.346 AC: 86766AN: 250680 AF XY: 0.343 show subpopulations
GnomAD4 exome AF: 0.349 AC: 510361AN: 1460910Hom.: 90417 Cov.: 35 AF XY: 0.347 AC XY: 252268AN XY: 726784 show subpopulations
GnomAD4 genome AF: 0.325 AC: 49439AN: 152046Hom.: 8359 Cov.: 32 AF XY: 0.324 AC XY: 24091AN XY: 74306 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 52% of patients studied by a panel of primary immunodeficiencies. Number of patients: 50. Only high quality variants are reported. -
Singleton-Merten syndrome 2 Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at