chr2-54255705-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001003937.3(TSPYL6):c.447C>T(p.Asp149=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,613,818 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0078 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00082 ( 15 hom. )
Consequence
TSPYL6
NM_001003937.3 synonymous
NM_001003937.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.224
Genes affected
TSPYL6 (HGNC:14521): (TSPY like 6) Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in nucleosome assembly. Predicted to be active in chromatin and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
ACYP2 (HGNC:180): (acylphosphatase 2) Acylphosphatase can hydrolyze the phosphoenzyme intermediate of different membrane pumps, particularly the Ca2+/Mg2+-ATPase from sarcoplasmic reticulum of skeletal muscle. Two isoenzymes have been isolated, called muscle acylphosphatase and erythrocyte acylphosphatase on the basis of their tissue localization. This gene encodes the muscle-type isoform (MT). An increase of the MT isoform is associated with muscle differentiation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
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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=-0.86).
BP6
Variant 2-54255705-G-A is Benign according to our data. Variant chr2-54255705-G-A is described in ClinVar as [Benign]. Clinvar id is 773481.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.224 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00779 (1186/152150) while in subpopulation AFR AF= 0.0275 (1140/41508). AF 95% confidence interval is 0.0261. There are 15 homozygotes in gnomad4. There are 575 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPYL6 | NM_001003937.3 | c.447C>T | p.Asp149= | synonymous_variant | 1/1 | ENST00000317802.9 | |
ACYP2 | NM_001320586.2 | c.405-48983G>A | intron_variant | ENST00000607452.6 | |||
LOC105374610 | XR_007086321.1 | n.1296-16421C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPYL6 | ENST00000317802.9 | c.447C>T | p.Asp149= | synonymous_variant | 1/1 | NM_001003937.3 | P1 | ||
ACYP2 | ENST00000607452.6 | c.405-48983G>A | intron_variant | 2 | NM_001320586.2 |
Frequencies
GnomAD3 genomes AF: 0.00771 AC: 1172AN: 152032Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00192 AC: 479AN: 249142Hom.: 4 AF XY: 0.00151 AC XY: 204AN XY: 135226
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GnomAD4 exome AF: 0.000823 AC: 1203AN: 1461668Hom.: 15 Cov.: 33 AF XY: 0.000730 AC XY: 531AN XY: 727136
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GnomAD4 genome AF: 0.00779 AC: 1186AN: 152150Hom.: 15 Cov.: 32 AF XY: 0.00773 AC XY: 575AN XY: 74362
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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 | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at