7-5622913-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_207111.4(RNF216):āc.2719C>Gā(p.Leu907Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,613,080 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (ā ).
Frequency
Consequence
NM_207111.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF216 | NM_207111.4 | c.2719C>G | p.Leu907Val | missense_variant | 17/17 | ENST00000389902.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF216 | ENST00000389902.8 | c.2719C>G | p.Leu907Val | missense_variant | 17/17 | 1 | NM_207111.4 | P4 | |
RNF216 | ENST00000425013.6 | c.2548C>G | p.Leu850Val | missense_variant | 17/17 | 1 | A1 | ||
RNF216 | ENST00000389900.8 | c.*1836C>G | 3_prime_UTR_variant, NMD_transcript_variant | 16/16 | 1 | ||||
RNF216 | ENST00000469375.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000160 AC: 40AN: 250746Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135436
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1460708Hom.: 1 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 726454
GnomAD4 genome AF: 0.000545 AC: 83AN: 152372Hom.: 0 Cov.: 32 AF XY: 0.000577 AC XY: 43AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at