1-926029-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001385641.1(SAMD11):c.609+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,609,122 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
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000010 ( 0 hom. )
Consequence
SAMD11
NM_001385641.1 intron
NM_001385641.1 intron
Scores
2
Splicing: ADA: 0.00007013
2
Clinical Significance
Conservation
PhyloP100: -0.653
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 Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 1-926029-C-T is Benign according to our data. Variant chr1-926029-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1624593.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMD11 | NM_001385641.1 | c.609+16C>T | intron_variant | Intron 2 of 13 | ENST00000616016.5 | NP_001372570.1 | ||
SAMD11 | NM_001385640.1 | c.609+16C>T | intron_variant | Intron 2 of 13 | NP_001372569.1 | |||
SAMD11 | NM_152486.4 | c.72+16C>T | 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.609+16C>T | intron_variant | Intron 2 of 13 | 5 | NM_001385641.1 | ENSP00000478421.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247504Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134572
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GnomAD4 exome AF: 0.0000103 AC: 15AN: 1456890Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 4AN XY: 724984
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74386
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 19, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at