1-40202572-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_012421.4(RLF):āc.768A>Gā(p.Thr256=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000969 in 1,559,008 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0051 ( 6 hom., cov: 32)
Exomes š: 0.00052 ( 6 hom. )
Consequence
RLF
NM_012421.4 synonymous
NM_012421.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.198
Genes affected
RLF (HGNC:10025): (RLF zinc finger) Predicted to enable DNA binding activity and DNA-binding transcription activator activity, RNA polymerase II-specific. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within histone H3-K4 monomethylation and regulation of DNA methylation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 1-40202572-A-G is Benign according to our data. Variant chr1-40202572-A-G is described in ClinVar as [Benign]. Clinvar id is 726801.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.198 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00507 (773/152330) while in subpopulation AFR AF= 0.0173 (718/41574). AF 95% confidence interval is 0.0162. There are 6 homozygotes in gnomad4. There are 387 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 773 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RLF | NM_012421.4 | c.768A>G | p.Thr256= | synonymous_variant | 5/8 | ENST00000372771.5 | |
RLF | XM_047427055.1 | c.120A>G | p.Thr40= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RLF | ENST00000372771.5 | c.768A>G | p.Thr256= | synonymous_variant | 5/8 | 1 | NM_012421.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00505 AC: 768AN: 152212Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00144 AC: 288AN: 199884Hom.: 3 AF XY: 0.00103 AC XY: 113AN XY: 109952
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GnomAD4 exome AF: 0.000525 AC: 738AN: 1406678Hom.: 6 Cov.: 29 AF XY: 0.000472 AC XY: 330AN XY: 699186
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GnomAD4 genome ? AF: 0.00507 AC: 773AN: 152330Hom.: 6 Cov.: 32 AF XY: 0.00520 AC XY: 387AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at