rs17004911
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015330.6(SPECC1L):c.3088-14317C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 152,204 control chromosomes in the GnomAD database, including 177 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 0.034 ( 177 hom., cov: 32)
Consequence
SPECC1L
NM_015330.6 intron
NM_015330.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.492
Genes affected
SPECC1L (HGNC:29022): (sperm antigen with calponin homology and coiled-coil domains 1 like) This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and the downstream ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]
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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=-0.55).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPECC1L | NM_015330.6 | c.3088-14317C>G | intron_variant | ENST00000314328.14 | |||
SPECC1L-ADORA2A | NR_103546.1 | n.3518-14317C>G | intron_variant, non_coding_transcript_variant | ||||
LOC105372960 | XR_938082.3 | n.136-2935G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPECC1L | ENST00000314328.14 | c.3088-14317C>G | intron_variant | 1 | NM_015330.6 | P1 | |||
SPECC1L | ENST00000437398.5 | c.3088-14317C>G | intron_variant | 1 | P1 | ||||
SPECC1L | ENST00000541492.1 | c.3088-15377C>G | intron_variant | 2 | |||||
SPECC1L | ENST00000651059.1 | c.3145-14317C>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0335 AC: 5093AN: 152086Hom.: 175 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0336 AC: 5117AN: 152204Hom.: 177 Cov.: 32 AF XY: 0.0326 AC XY: 2424AN XY: 74412
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3478
ClinVar
Not reported inComputational scores
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Name
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Prediction
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