chr1-930081-A-AGCCCCACCTTCCTCTCCTCCT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_001385641.1(SAMD11):c.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,475,002 control chromosomes in the GnomAD database, including 16 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00047 ( 16 hom. )
Consequence
SAMD11
NM_001385641.1 splice_acceptor, intron
NM_001385641.1 splice_acceptor, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.291
Genes affected
SAMD11 (HGNC:28706): (sterile alpha motif domain containing 11) Predicted to enable several functions, including histone binding activity; protein domain specific binding activity; and protein self-association. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000473 (626/1323458) while in subpopulation EAS AF= 0.0169 (589/34838). AF 95% confidence interval is 0.0158. There are 16 homozygotes in gnomad4_exome. There are 320 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 16 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMD11 | NM_001385641.1 | c.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC | splice_acceptor_variant, intron_variant | Intron 2 of 13 | ENST00000616016.5 | NP_001372570.1 | ||
SAMD11 | NM_001385640.1 | c.610-23_610-3dupTTCCTCTCCTCCTGCCCCACC | splice_acceptor_variant, intron_variant | Intron 2 of 13 | NP_001372569.1 | |||
SAMD11 | NM_152486.4 | c.73-23_73-3dupTTCCTCTCCTCCTGCCCCACC | splice_acceptor_variant, intron_variant | Intron 2 of 13 | NP_689699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMD11 | ENST00000616016.5 | c.610-74_610-73insGCCCCACCTTCCTCTCCTCCT | intron_variant | Intron 2 of 13 | 5 | NM_001385641.1 | ENSP00000478421.2 |
Frequencies
GnomAD3 genomes AF: 0.000198 AC: 30AN: 151426Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000473 AC: 626AN: 1323458Hom.: 16 AF XY: 0.000494 AC XY: 320AN XY: 647992
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GnomAD4 genome AF: 0.000198 AC: 30AN: 151544Hom.: 0 Cov.: 33 AF XY: 0.000162 AC XY: 12AN XY: 74028
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at