rs7443175
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001127496.3(SPRY4):c.-47-729A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,150 control chromosomes in the GnomAD database, including 35,979 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 0.66 ( 35973 hom., cov: 33)
Exomes 𝑓: 0.77 ( 6 hom. )
Consequence
SPRY4
NM_001127496.3 intron
NM_001127496.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0770
Genes affected
SPRY4 (HGNC:15533): (sprouty RTK signaling antagonist 4) This gene encodes a member of a family of cysteine- and proline-rich proteins. The encoded protein is an inhibitor of the receptor-transduced mitogen-activated protein kinase (MAPK) signaling pathway. Activity of this protein impairs the formation of active GTP-RAS. Nucleotide variation in this gene has been associated with hypogonadotropic hypogonadism 17 with or without anosmia. Alternative splicing results in a multiple transcript variants. [provided by RefSeq, Jun 2014]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPRY4 | NM_001127496.3 | c.-47-729A>G | intron_variant | ENST00000434127.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPRY4 | ENST00000434127.3 | c.-47-729A>G | intron_variant | 1 | NM_001127496.3 | P1 | |||
SPRY4 | ENST00000344120.4 | c.23-729A>G | intron_variant | 1 | |||||
SPRY4 | ENST00000511815.1 | c.-47-729A>G | intron_variant | 4 | |||||
SPRY4 | ENST00000503582.1 | n.529-729A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.663 AC: 100810AN: 152010Hom.: 35952 Cov.: 33
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GnomAD4 exome AF: 0.773 AC: 17AN: 22Hom.: 6 AF XY: 0.800 AC XY: 8AN XY: 10
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GnomAD4 genome ? AF: 0.663 AC: 100849AN: 152128Hom.: 35973 Cov.: 33 AF XY: 0.667 AC XY: 49646AN XY: 74382
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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