rs17154769
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004225.3(MFHAS1):c.2999-4558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,152 control chromosomes in the GnomAD database, including 6,246 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 0.22 ( 6246 hom., cov: 33)
Consequence
MFHAS1
NM_004225.3 intron
NM_004225.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0400
Genes affected
MFHAS1 (HGNC:16982): (multifunctional ROCO family signaling regulator 1) Identified in a human 8p amplicon, this gene is a potential oncogene whose expression is enhanced in some malignant fibrous histiocytomas (MFH). The primary structure of its product includes an ATP/GTP-binding site, three leucine zipper domains, and a leucine-rich tandem repeat, which are structural or functional elements for interactions among proteins related to the cell cycle, and which suggest that overexpression might be oncogenic with respect to MFH. [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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFHAS1 | NM_004225.3 | c.2999-4558T>C | intron_variant | ENST00000276282.7 | |||
MFHAS1 | XM_047422419.1 | c.2999-4558T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFHAS1 | ENST00000276282.7 | c.2999-4558T>C | intron_variant | 1 | NM_004225.3 | P1 | |||
MFHAS1 | ENST00000520091.1 | n.317-4558T>C | intron_variant, non_coding_transcript_variant | 4 | |||||
MFHAS1 | ENST00000520715.5 | n.46-4558T>C | intron_variant, non_coding_transcript_variant | 3 | |||||
MFHAS1 | ENST00000521881.5 | n.43-4558T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.218 AC: 33207AN: 152034Hom.: 6225 Cov.: 33
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.219 AC: 33262AN: 152152Hom.: 6246 Cov.: 33 AF XY: 0.216 AC XY: 16055AN XY: 74404
GnomAD4 genome
?
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33262
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152152
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33
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16055
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74404
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557
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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