chr20-33001288-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_080675.4(SUN5):c.212-10T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,568,184 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
SUN5
NM_080675.4 splice_polypyrimidine_tract, intron
NM_080675.4 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.005790
2
Clinical Significance
Conservation
PhyloP100: 1.00
Genes affected
SUN5 (HGNC:16252): (Sad1 and UNC84 domain containing 5) The protein encoded by this gene appears to play a role in the meiotic stage of spermatogenesis. The encoded protein localizes to the junction between the sperm head and body and may be involved in nuclear envelope reconstitution and nuclear migration. Mutations in this gene have been implicated in acephalic spermatozoa syndrome. [provided by RefSeq, May 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 20-33001288-A-G is Benign according to our data. Variant chr20-33001288-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3040125.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUN5 | NM_080675.4 | c.212-10T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000356173.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUN5 | ENST00000356173.8 | c.212-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_080675.4 | P2 | |||
SUN5 | ENST00000375519.2 | c.212-1153T>C | intron_variant | 2 | |||||
SUN5 | ENST00000375523.7 | c.137-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | A2 | ||||
SUN5 | ENST00000420875.5 | c.179-10T>C | splice_polypyrimidine_tract_variant, intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152066Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000442 AC: 8AN: 180968Hom.: 0 AF XY: 0.0000417 AC XY: 4AN XY: 95872
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GnomAD4 exome AF: 0.000186 AC: 263AN: 1416118Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 113AN XY: 699942
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GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152066Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74274
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SUN5-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 26, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: -10
Find out detailed SpliceAI scores and Pangolin per-transcript scores at