rs17173769
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000356800.6(SMARCD3):c.40-14672A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 152,282 control chromosomes in the GnomAD database, including 165 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.031 ( 165 hom., cov: 32)
Consequence
SMARCD3
ENST00000356800.6 intron
ENST00000356800.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.129
Genes affected
SMARCD3 (HGNC:11108): (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3) The protein encoded by this gene is a member of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI and has sequence similarity to the yeast Swp73 protein. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0984 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCD3 | NM_001003802.2 | c.40-14672A>G | intron_variant | ||||
SMARCD3 | NM_003078.4 | c.40-14672A>G | intron_variant | ||||
SMARCD3 | XM_047420758.1 | c.-17+14771A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCD3 | ENST00000356800.6 | c.40-14672A>G | intron_variant | 1 | |||||
SMARCD3 | ENST00000392811.6 | c.40-14672A>G | intron_variant | 1 | |||||
SMARCD3 | ENST00000491651.1 | c.40-14672A>G | intron_variant | 4 | |||||
SMARCD3 | ENST00000469154.5 | c.70+14771A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0313 AC: 4768AN: 152162Hom.: 165 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0313 AC: 4768AN: 152282Hom.: 165 Cov.: 32 AF XY: 0.0326 AC XY: 2427AN XY: 74460
GnomAD4 genome
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138
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at