4-75957574-G-C
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_018115.4(SDAD1):āc.1713C>Gā(p.Ala571=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,614,092 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0019 ( 7 hom., cov: 32)
Exomes š: 0.0014 ( 37 hom. )
Consequence
SDAD1
NM_018115.4 synonymous
NM_018115.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0650
Genes affected
SDAD1 (HGNC:25537): (SDA1 domain containing 1) Predicted to be involved in ribosomal large subunit biogenesis and ribosomal large subunit export from nucleus. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant 4-75957574-G-C is Benign according to our data. Variant chr4-75957574-G-C is described in ClinVar as [Benign]. Clinvar id is 773696.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.065 with no splicing effect.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00187 (285/152200) while in subpopulation EAS AF= 0.0482 (250/5182). AF 95% confidence interval is 0.0433. There are 7 homozygotes in gnomad4. There are 163 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDAD1 | NM_018115.4 | c.1713C>G | p.Ala571= | synonymous_variant | 19/22 | ENST00000356260.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDAD1 | ENST00000356260.10 | c.1713C>G | p.Ala571= | synonymous_variant | 19/22 | 1 | NM_018115.4 | P1 | |
SDAD1 | ENST00000395710.5 | c.*1569C>G | 3_prime_UTR_variant, NMD_transcript_variant | 19/22 | 1 | ||||
SDAD1 | ENST00000395711.8 | c.1602C>G | p.Ala534= | synonymous_variant | 18/21 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 288AN: 152082Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00336 AC: 846AN: 251456Hom.: 20 AF XY: 0.00327 AC XY: 444AN XY: 135900
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GnomAD4 exome AF: 0.00136 AC: 1981AN: 1461892Hom.: 37 Cov.: 35 AF XY: 0.00138 AC XY: 1006AN XY: 727248
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GnomAD4 genome AF: 0.00187 AC: 285AN: 152200Hom.: 7 Cov.: 32 AF XY: 0.00219 AC XY: 163AN XY: 74406
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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 | Jan 05, 2018 | - - |
Computational scores
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Benign
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at