chr17-63832999-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001098426.2(SMARCD2):c.1543-8T>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000498 in 1,587,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001098426.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMARCD2 | NM_001098426.2 | c.1543-8T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000448276.7 | |||
SMARCD2 | NM_001330439.1 | c.1318-8T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SMARCD2 | NM_001330440.2 | c.1399-8T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCD2 | ENST00000448276.7 | c.1543-8T>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001098426.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000855 AC: 18AN: 210632Hom.: 0 AF XY: 0.0000705 AC XY: 8AN XY: 113416
GnomAD4 exome AF: 0.0000320 AC: 46AN: 1435350Hom.: 0 Cov.: 33 AF XY: 0.0000337 AC XY: 24AN XY: 711646
GnomAD4 genome AF: 0.000217 AC: 33AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
SMARCD2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 30, 2023 | 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