11-65579427-C-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001099409.3(EHBP1L1):āc.249C>Gā(p.Thr83Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000641 in 1,543,936 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00042 ( 0 hom., cov: 30)
Exomes š: 0.00067 ( 2 hom. )
Consequence
EHBP1L1
NM_001099409.3 synonymous
NM_001099409.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.81
Genes affected
EHBP1L1 (HGNC:30682): (EH domain binding protein 1 like 1) Predicted to be involved in actin cytoskeleton organization. Located in 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=-0.69).
BP6
Variant 11-65579427-C-G is Benign according to our data. Variant chr11-65579427-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2641961.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.81 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EHBP1L1 | NM_001099409.3 | c.249C>G | p.Thr83Thr | synonymous_variant | 3/19 | ENST00000309295.9 | NP_001092879.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EHBP1L1 | ENST00000309295.9 | c.249C>G | p.Thr83Thr | synonymous_variant | 3/19 | 1 | NM_001099409.3 | ENSP00000312671.4 | ||
EHBP1L1 | ENST00000533237.5 | c.249C>G | p.Thr83Thr | synonymous_variant | 3/12 | 5 | ENSP00000431996.1 | |||
EHBP1L1 | ENST00000634639.1 | c.249C>G | p.Thr83Thr | synonymous_variant | 3/12 | 5 | ENSP00000489002.1 | |||
EHBP1L1 | ENST00000531106.1 | n.*47C>G | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000421 AC: 64AN: 151962Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000463 AC: 74AN: 159832Hom.: 1 AF XY: 0.000624 AC XY: 53AN XY: 84898
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GnomAD4 exome AF: 0.000665 AC: 926AN: 1391856Hom.: 2 Cov.: 32 AF XY: 0.000669 AC XY: 459AN XY: 685640
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GnomAD4 genome AF: 0.000421 AC: 64AN: 152080Hom.: 0 Cov.: 30 AF XY: 0.000363 AC XY: 27AN XY: 74322
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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 | EHBP1L1: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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