1-40161420-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_012421.4(RLF):āc.21C>Gā(p.Asp7Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,546,468 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (ā ).
Frequency
Consequence
NM_012421.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RLF | NM_012421.4 | c.21C>G | p.Asp7Glu | missense_variant | 1/8 | ENST00000372771.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RLF | ENST00000372771.5 | c.21C>G | p.Asp7Glu | missense_variant | 1/8 | 1 | NM_012421.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000340 AC: 6AN: 176276Hom.: 0 AF XY: 0.0000305 AC XY: 3AN XY: 98520
GnomAD4 exome AF: 0.0000122 AC: 17AN: 1394372Hom.: 0 Cov.: 31 AF XY: 0.0000130 AC XY: 9AN XY: 691296
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.21C>G (p.D7E) alteration is located in exon 1 (coding exon 1) of the RLF gene. This alteration results from a C to G substitution at nucleotide position 21, causing the aspartic acid (D) at amino acid position 7 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at