chr19-49645071-G-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_021228.3(SCAF1):c.45G>C(p.Gly15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,154 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 28 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 36 hom. )
Consequence
SCAF1
NM_021228.3 synonymous
NM_021228.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.902
Genes affected
SCAF1 (HGNC:30403): (SR-related CTD associated factor 1) Enables RNA polymerase II C-terminal domain binding activity. Predicted to be involved in RNA splicing; mRNA processing; and transcription by RNA polymerase II. Predicted to be located 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=-0.73).
BP6
?
Variant 19-49645071-G-C is Benign according to our data. Variant chr19-49645071-G-C is described in ClinVar as [Benign]. Clinvar id is 769038.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.902 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (1752/152320) while in subpopulation AFR AF= 0.0394 (1639/41568). AF 95% confidence interval is 0.0378. There are 28 homozygotes in gnomad4. There are 838 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAF1 | NM_021228.3 | c.45G>C | p.Gly15= | synonymous_variant | 2/11 | ENST00000360565.8 | |
SCAF1 | XM_011527194.4 | c.54G>C | p.Gly18= | synonymous_variant | 2/11 | ||
SCAF1 | XM_005259122.6 | c.45G>C | p.Gly15= | synonymous_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAF1 | ENST00000360565.8 | c.45G>C | p.Gly15= | synonymous_variant | 2/11 | 2 | NM_021228.3 | P1 | |
SCAF1 | ENST00000598359.5 | c.45G>C | p.Gly15= | synonymous_variant | 2/7 | 3 | |||
SCAF1 | ENST00000595242.3 | c.45G>C | p.Gly15= | synonymous_variant | 1/4 | 3 | |||
SCAF1 | ENST00000601038.5 | c.45G>C | p.Gly15= | synonymous_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0115 AC: 1744AN: 152202Hom.: 26 Cov.: 32
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GnomAD3 exomes AF: 0.00309 AC: 775AN: 251096Hom.: 11 AF XY: 0.00231 AC XY: 314AN XY: 135756
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GnomAD4 exome AF: 0.00124 AC: 1813AN: 1461834Hom.: 36 Cov.: 31 AF XY: 0.00109 AC XY: 793AN XY: 727224
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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 | Jun 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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