rs3737861
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030663.3(SMCP):c.-21+16A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,540 control chromosomes in the GnomAD database, including 13,889 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.36 ( 13885 hom., cov: 32)
Exomes 𝑓: 0.14 ( 4 hom. )
Consequence
SMCP
NM_030663.3 intron
NM_030663.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.317
Genes affected
SMCP (HGNC:6962): (sperm mitochondria associated cysteine rich protein) Sperm mitochondria differ in morphology and subcellular localization from those of somatic cells. They are elongated, flattened, and arranged circumferentially to form a helical coiled sheath in the midpiece of the sperm flagellum. The protein encoded by this gene localizes to the capsule associated with the mitochondrial outer membranes and is thought to function in the organization and stabilization of the helical structure of the sperm's mitochondrial sheath. [provided by RefSeq, Jul 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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMCP | NM_030663.3 | c.-21+16A>C | intron_variant | ENST00000368765.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMCP | ENST00000368765.4 | c.-21+16A>C | intron_variant | 1 | NM_030663.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.355 AC: 53953AN: 151946Hom.: 13838 Cov.: 32
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GnomAD4 exome AF: 0.145 AC: 69AN: 476Hom.: 4 Cov.: 0 AF XY: 0.143 AC XY: 42AN XY: 294
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GnomAD4 genome AF: 0.356 AC: 54059AN: 152064Hom.: 13885 Cov.: 32 AF XY: 0.354 AC XY: 26289AN XY: 74340
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ClinVar
Not reported inComputational scores
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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