14-54755757-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015589.6(SAMD4A):c.1176+4220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,956 control chromosomes in the GnomAD database, including 18,060 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (★).
Frequency
Genomes: 𝑓 0.47 ( 18060 hom., cov: 31)
Consequence
SAMD4A
NM_015589.6 intron
NM_015589.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.260
Genes affected
SAMD4A (HGNC:23023): (sterile alpha motif domain containing 4A) Sterile alpha motifs (SAMs) in proteins such as SAMD4A are part of an RNA-binding domain that functions as a posttranscriptional regulator by binding to an RNA sequence motif known as the Smaug recognition element, which was named after the Drosophila Smaug protein (Baez and Boccaccio, 2005 [PubMed 16221671]).[supplied by OMIM, Mar 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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMD4A | NM_015589.6 | c.1176+4220T>C | intron_variant | ENST00000554335.6 | NP_056404.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMD4A | ENST00000554335.6 | c.1176+4220T>C | intron_variant | 5 | NM_015589.6 | ENSP00000452535.1 |
Frequencies
GnomAD3 genomes AF: 0.474 AC: 71909AN: 151838Hom.: 18058 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.473 AC: 71931AN: 151956Hom.: 18060 Cov.: 31 AF XY: 0.465 AC XY: 34489AN XY: 74248
GnomAD4 genome
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ClinVar
Significance: association
Submissions summary: Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Lip and oral cavity carcinoma Other:1
association, criteria provided, single submitter | case-control | Department of Biological Science, Sunandan Divatia School of Science, NMIMS University | - | A significant association of rs1957358 (SAMD4A) TT (odds ratio [OR] 1.44; 95% confidence interval [CI] 1.10-1.90) indicated increased risk to oral cancer. While, rs1957358 (SAMD4A) TC (odds ratio [OR] 0.67; 95% confidence interval [CI] 0.53-0.87) indicated decreased risk to oral cancer. - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at