3-47590670-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003074.4(SMARCC1):c.3211A>G(p.Asn1071Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000467 in 1,542,432 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 Uncertain significance (★).
Frequency
Consequence
NM_003074.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMARCC1 | ENST00000254480.10 | c.3211A>G | p.Asn1071Asp | missense_variant | Exon 27 of 28 | 1 | NM_003074.4 | ENSP00000254480.5 | ||
SMARCC1 | ENST00000425518.5 | n.3101A>G | non_coding_transcript_exon_variant | Exon 27 of 28 | 2 | |||||
SMARCC1 | ENST00000492896.1 | n.*136A>G | downstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000568 AC: 11AN: 193500Hom.: 0 AF XY: 0.0000660 AC XY: 7AN XY: 106062
GnomAD4 exome AF: 0.0000360 AC: 50AN: 1390176Hom.: 0 Cov.: 30 AF XY: 0.0000421 AC XY: 29AN XY: 688608
GnomAD4 genome AF: 0.000144 AC: 22AN: 152256Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74454
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.3211A>G (p.N1071D) alteration is located in exon 27 (coding exon 27) of the SMARCC1 gene. This alteration results from a A to G substitution at nucleotide position 3211, causing the asparagine (N) at amino acid position 1071 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at