chr15-45402570-G-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_024063.3(SPATA5L1):c.141G>T(p.Val47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 1,579,392 control chromosomes in the GnomAD database, including 6,954 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.12 ( 3644 hom., cov: 33)
Exomes 𝑓: 0.014 ( 3310 hom. )
Consequence
SPATA5L1
NM_024063.3 synonymous
NM_024063.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.994
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 15-45402570-G-T is Benign according to our data. Variant chr15-45402570-G-T is described in ClinVar as [Benign]. Clinvar id is 1235297.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.994 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATA5L1 | NM_024063.3 | c.141G>T | p.Val47= | synonymous_variant | 1/8 | ENST00000305560.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG2B | ENST00000305560.11 | c.141G>T | p.Val47= | synonymous_variant | 1/8 | 1 | NM_024063.3 | P1 | |
AFG2B | ENST00000559860.2 | n.201G>T | non_coding_transcript_exon_variant | 1/5 | 2 | ||||
AFG2B | ENST00000531970.5 | c.141G>T | p.Val47= | synonymous_variant, NMD_transcript_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.119 AC: 18132AN: 152126Hom.: 3617 Cov.: 33
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GnomAD3 exomes AF: 0.0316 AC: 5759AN: 182076Hom.: 938 AF XY: 0.0278 AC XY: 2780AN XY: 100156
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GnomAD4 exome AF: 0.0144 AC: 20546AN: 1427148Hom.: 3310 Cov.: 33 AF XY: 0.0139 AC XY: 9859AN XY: 707752
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GnomAD4 genome AF: 0.120 AC: 18202AN: 152244Hom.: 3644 Cov.: 33 AF XY: 0.115 AC XY: 8598AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at