chr4-143514077-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003601.4(SMARCA5):c.153T>G(p.Ala51=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SMARCA5
NM_003601.4 synonymous
NM_003601.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.47
Genes affected
SMARCA5 (HGNC:11101): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5) The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The protein encoded by this gene is a component of the chromatin remodeling and spacing factor RSF, a facilitator of the transcription of class II genes by RNA polymerase II. The encoded protein is similar in sequence to the Drosophila ISWI chromatin remodeling protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 4-143514077-T-G is Benign according to our data. Variant chr4-143514077-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 728189.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.47 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCA5 | NM_003601.4 | c.153T>G | p.Ala51= | synonymous_variant | 1/24 | ENST00000283131.4 | |
SMARCA5-AS1 | NR_104027.1 | n.542A>C | non_coding_transcript_exon_variant | 2/2 | |||
SMARCA5 | XM_047416323.1 | c.153T>G | p.Ala51= | synonymous_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCA5 | ENST00000283131.4 | c.153T>G | p.Ala51= | synonymous_variant | 1/24 | 1 | NM_003601.4 | P1 | |
SMARCA5-AS1 | ENST00000500800.2 | n.340A>C | non_coding_transcript_exon_variant | 2/2 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000209 AC: 29AN: 1387226Hom.: 0 Cov.: 31 AF XY: 0.0000189 AC XY: 13AN XY: 687618
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
29
AN:
1387226
Hom.:
Cov.:
31
AF XY:
AC XY:
13
AN XY:
687618
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 13, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at