rs10498874
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001044305.3(SMAP1):c.253-7630A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,058 control chromosomes in the GnomAD database, including 14,742 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 0.43 ( 14742 hom., cov: 32)
Consequence
SMAP1
NM_001044305.3 intron
NM_001044305.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.225
Genes affected
SMAP1 (HGNC:19651): (small ArfGAP 1) The protein encoded by this gene is similar to the mouse stromal membrane-associated protein-1. This similarity suggests that this human gene product is also a type II membrane glycoprotein involved in the erythropoietic stimulatory activity of stromal cells. Alternate splicing results in multiple transcript variants encoding different isoforms. [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=-0.91).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAP1 | NM_001044305.3 | c.253-7630A>C | intron_variant | ENST00000370455.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAP1 | ENST00000370455.8 | c.253-7630A>C | intron_variant | 1 | NM_001044305.3 | P3 | |||
SMAP1 | ENST00000316999.9 | c.253-7630A>C | intron_variant | 1 | A1 | ||||
SMAP1 | ENST00000619054.4 | c.223-7630A>C | intron_variant | 1 | |||||
SMAP1 | ENST00000370452.7 | c.253-7630A>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.435 AC: 66090AN: 151940Hom.: 14743 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: 0.435 AC: 66102AN: 152058Hom.: 14742 Cov.: 32 AF XY: 0.433 AC XY: 32168AN XY: 74324
GnomAD4 genome
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32
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32168
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74324
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1301
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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