chr2-185738835-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173651.4(FSIP2):c.-60G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000723 in 1,383,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
FSIP2
NM_173651.4 5_prime_UTR
NM_173651.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0670
Genes affected
FSIP2 (HGNC:21675): (fibrous sheath interacting protein 2) This gene encodes a protein associated with the sperm fibrous sheath. Genes encoding most of the fibrous-sheath associated proteins genes are transcribed only during the postmeiotic period of spermatogenesis. The protein encoded by this gene is specific to spermatogenic cells. Copy number variation in this gene may be associated with testicular germ cell tumors. Pseudogenes associated with this gene are reported on chromosomes 2 and X. [provided by RefSeq, Aug 2016]
FSIP2-AS2 (HGNC:54061): (FSIP2 antisense RNA 2)
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FSIP2 | NM_173651.4 | c.-60G>A | 5_prime_UTR_variant | 1/23 | ENST00000424728.6 | NP_775922.3 | ||
FSIP2-AS2 | NR_110217.1 | n.99+1544C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSIP2 | ENST00000424728.6 | c.-60G>A | 5_prime_UTR_variant | 1/23 | 5 | NM_173651.4 | ENSP00000401306 | P1 | ||
FSIP2-AS2 | ENST00000427269.2 | n.101+1544C>T | intron_variant, non_coding_transcript_variant | 5 | ||||||
FSIP2-AS1 | ENST00000667756.1 | n.37+49931C>T | intron_variant, non_coding_transcript_variant | |||||||
FSIP2-AS2 | ENST00000437717.1 | n.119+72C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000764 AC: 1AN: 130834Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 71310
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GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1383616Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 682774
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2022 | The c.208G>A (p.G70R) alteration is located in exon 1 (coding exon 1) of the FSIP2 gene. This alteration results from a G to A substitution at nucleotide position 208, causing the glycine (G) at amino acid position 70 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
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Name
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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