9-42183738-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001145196.1(SPATA31A6):c.51C>T(p.Asn17Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000411 in 1,534,826 control chromosomes in the GnomAD database, including 104 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00027 ( 3 hom., cov: 23)
Exomes 𝑓: 0.00042 ( 101 hom. )
Consequence
SPATA31A6
NM_001145196.1 synonymous
NM_001145196.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.278
Genes affected
SPATA31A6 (HGNC:32006): (SPATA31 subfamily A member 6) Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 9-42183738-C-T is Benign according to our data. Variant chr9-42183738-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659218.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.278 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 36AN: 133648Hom.: 3 Cov.: 23
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GnomAD4 exome AF: 0.000425 AC: 595AN: 1401178Hom.: 101 Cov.: 34 AF XY: 0.000409 AC XY: 285AN XY: 697382
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GnomAD4 genome AF: 0.000269 AC: 36AN: 133648Hom.: 3 Cov.: 23 AF XY: 0.000216 AC XY: 14AN XY: 64868
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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
Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
SPATA31A6: BS2 -
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