chr4-94252659-A-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_020159.5(SMARCAD1):āc.933A>Gā(p.Glu311=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00726 in 1,575,152 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0045 ( 6 hom., cov: 32)
Exomes š: 0.0076 ( 65 hom. )
Consequence
SMARCAD1
NM_020159.5 synonymous
NM_020159.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.10
Genes affected
SMARCAD1 (HGNC:18398): (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1) This gene encodes a member of the SNF subfamily of helicase proteins. The encoded protein plays a critical role in the restoration of heterochromatin organization and propagation of epigenetic patterns following DNA replication by mediating histone H3/H4 deacetylation. Mutations in this gene are associated with adermatoglyphia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 4-94252659-A-G is Benign according to our data. Variant chr4-94252659-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 789281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.1 with no splicing effect.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00447 (681/152320) while in subpopulation NFE AF= 0.00781 (531/68030). AF 95% confidence interval is 0.00726. There are 6 homozygotes in gnomad4. There are 307 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 681 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCAD1 | NM_020159.5 | c.933A>G | p.Glu311= | synonymous_variant | 9/24 | ENST00000354268.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCAD1 | ENST00000354268.9 | c.933A>G | p.Glu311= | synonymous_variant | 9/24 | 1 | NM_020159.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00447 AC: 681AN: 152202Hom.: 6 Cov.: 32
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GnomAD3 exomes AF: 0.00419 AC: 873AN: 208176Hom.: 11 AF XY: 0.00448 AC XY: 505AN XY: 112746
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GnomAD4 exome AF: 0.00756 AC: 10760AN: 1422832Hom.: 65 Cov.: 32 AF XY: 0.00724 AC XY: 5106AN XY: 705662
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GnomAD4 genome AF: 0.00447 AC: 681AN: 152320Hom.: 6 Cov.: 32 AF XY: 0.00412 AC XY: 307AN XY: 74490
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | SMARCAD1: BP4, BP7 - |
Computational scores
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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