chr11-95128472-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015036.3(ENDOD1):āc.396A>Gā(p.Thr132=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,614,236 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.0026 ( 1 hom., cov: 32)
Exomes š: 0.0032 ( 15 hom. )
Consequence
ENDOD1
NM_015036.3 synonymous
NM_015036.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.122
Genes affected
ENDOD1 (HGNC:29129): (endonuclease domain containing 1) Predicted to enable endonuclease activity; metal ion binding activity; and nucleic acid binding activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Located in extracellular exosome and membrane. [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=-0.87).
BP6
Variant 11-95128472-A-G is Benign according to our data. Variant chr11-95128472-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2642302.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-95128472-A-G is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.122 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENDOD1 | NM_015036.3 | c.396A>G | p.Thr132= | synonymous_variant | 2/2 | ENST00000278505.5 | NP_055851.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENDOD1 | ENST00000278505.5 | c.396A>G | p.Thr132= | synonymous_variant | 2/2 | 1 | NM_015036.3 | ENSP00000278505 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00259 AC: 394AN: 152228Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00236 AC: 588AN: 249534Hom.: 4 AF XY: 0.00264 AC XY: 358AN XY: 135370
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GnomAD4 exome AF: 0.00315 AC: 4610AN: 1461890Hom.: 15 Cov.: 34 AF XY: 0.00314 AC XY: 2285AN XY: 727246
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GnomAD4 genome AF: 0.00259 AC: 395AN: 152346Hom.: 1 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74500
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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
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | ENDOD1: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at