chr9-88129719-TCTG-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2
The NM_001350978.3(SPATA31C2):c.3315_3317delCAG(p.Ser1105del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,603,086 control chromosomes in the GnomAD database, including 47 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0033 ( 4 hom., cov: 28)
Exomes 𝑓: 0.0035 ( 43 hom. )
Consequence
SPATA31C2
NM_001350978.3 disruptive_inframe_deletion
NM_001350978.3 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0120
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001350978.3. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant 9-88129719-TCTG-T is Benign according to our data. Variant chr9-88129719-TCTG-T is described in ClinVar as [Likely_benign]. Clinvar id is 3898068.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATA31C2 | NM_001350978.3 | c.3315_3317delCAG | p.Ser1105del | disruptive_inframe_deletion | Exon 4 of 4 | ENST00000324915.6 | NP_001337907.1 | |
SPATA31C2 | NM_001166137.1 | c.3315_3317delCAG | p.Ser1105del | disruptive_inframe_deletion | Exon 4 of 4 | NP_001159609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATA31C2 | ENST00000324915.6 | c.3315_3317delCAG | p.Ser1105del | disruptive_inframe_deletion | Exon 4 of 4 | 6 | NM_001350978.3 | ENSP00000509734.1 | ||
SPATA31C2 | ENST00000675441.1 | c.3315_3317delCAG | p.Ser1105del | disruptive_inframe_deletion | Exon 4 of 4 | ENSP00000509164.1 |
Frequencies
GnomAD3 genomes AF: 0.00332 AC: 505AN: 151918Hom.: 4 Cov.: 28
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GnomAD3 exomes AF: 0.00363 AC: 901AN: 248356Hom.: 9 AF XY: 0.00373 AC XY: 504AN XY: 135020
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GnomAD4 exome AF: 0.00353 AC: 5127AN: 1451048Hom.: 43 AF XY: 0.00347 AC XY: 2501AN XY: 721700
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GnomAD4 genome AF: 0.00332 AC: 505AN: 152038Hom.: 4 Cov.: 28 AF XY: 0.00365 AC XY: 271AN XY: 74288
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SPATA31C2: PM4:Supporting, BS2 -
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at