rs374677046
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003072.5(SMARCA4):c.4911+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,550,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003072.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCA4 | ENST00000646693.2 | c.5007+9G>A | intron_variant | Intron 35 of 35 | NM_001387283.1 | ENSP00000495368.1 | ||||
SMARCA4 | ENST00000344626.10 | c.4911+9G>A | intron_variant | Intron 34 of 34 | 1 | NM_003072.5 | ENSP00000343896.4 | |||
SMARCA4 | ENST00000643549.1 | c.4917+9G>A | intron_variant | Intron 34 of 34 | ENSP00000493975.1 | |||||
SMARCA4 | ENST00000541122.6 | c.4821+9G>A | intron_variant | Intron 34 of 34 | 5 | ENSP00000445036.2 | ||||
SMARCA4 | ENST00000643296.1 | c.4821+9G>A | intron_variant | Intron 33 of 33 | ENSP00000496635.1 | |||||
SMARCA4 | ENST00000644737.1 | c.4821+9G>A | intron_variant | Intron 33 of 33 | ENSP00000495548.1 | |||||
SMARCA4 | ENST00000589677.5 | c.4818+9G>A | intron_variant | Intron 34 of 34 | 5 | ENSP00000464778.1 | ||||
SMARCA4 | ENST00000643995.1 | c.4332+9G>A | intron_variant | Intron 31 of 31 | ENSP00000496004.1 | |||||
SMARCA4 | ENST00000644963.1 | c.3561+9G>A | intron_variant | Intron 27 of 27 | ENSP00000495599.1 | |||||
SMARCA4 | ENST00000644065.1 | c.3543+9G>A | intron_variant | Intron 26 of 26 | ENSP00000493615.1 | |||||
SMARCA4 | ENST00000642350.1 | c.3405+9G>A | intron_variant | Intron 26 of 26 | ENSP00000495355.1 | |||||
SMARCA4 | ENST00000643857.1 | c.3171+9G>A | intron_variant | Intron 24 of 24 | ENSP00000494159.1 | |||||
SMARCA4 | ENST00000538456.4 | c.975+9G>A | intron_variant | Intron 7 of 7 | 3 | ENSP00000495197.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000389 AC: 6AN: 154326Hom.: 0 AF XY: 0.0000245 AC XY: 2AN XY: 81494
GnomAD4 exome AF: 0.0000207 AC: 29AN: 1398202Hom.: 0 Cov.: 33 AF XY: 0.0000174 AC XY: 12AN XY: 689622
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
Rhabdoid tumor predisposition syndrome 2 Benign:1
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not provided Benign:1
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SMARCA4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at