6-81752010-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCG-ACCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCGCCGCCGAAGTCGCCG
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4BP6_Very_StrongBA1
The NM_017633.3(TENT5A):c.131_132insCGGCGACTTCGGCGG(p.Asp41_Gly45dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,339,720 control chromosomes in the GnomAD database, including 108,731 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G44G) has been classified as Benign.
Frequency
Consequence
NM_017633.3 inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT5A | NM_017633.3 | c.131_132insCGGCGACTTCGGCGG | p.Asp41_Gly45dup | inframe_insertion | 2/3 | ENST00000320172.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5A | ENST00000320172.11 | c.131_132insCGGCGACTTCGGCGG | p.Asp41_Gly45dup | inframe_insertion | 2/3 | 1 | NM_017633.3 | A2 | |
TENT5A | ENST00000369754.7 | c.188_189insCGGCGACTTCGGCGG | p.Asp60_Gly64dup | inframe_insertion | 2/3 | 1 | P4 | ||
TENT5A | ENST00000369756.3 | c.374_375insCGGCGACTTCGGCGG | p.Asp122_Gly126dup | inframe_insertion | 2/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.448 AC: 62497AN: 139368Hom.: 15272 Cov.: 0
GnomAD4 exome AF: 0.273 AC: 327410AN: 1200274Hom.: 93440 Cov.: 34 AF XY: 0.278 AC XY: 167481AN XY: 602742
GnomAD4 genome AF: 0.449 AC: 62545AN: 139446Hom.: 15291 Cov.: 0 AF XY: 0.447 AC XY: 30190AN XY: 67570
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Osteogenesis imperfecta, type 18 Benign:2
Benign, criteria provided, single submitter | clinical testing | Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital | Jul 19, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | May 04, 2023 | African/African American population allele frequency is 50.47% (rs373591596, 3735/7202 alleles, 1066 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.4.0, this variant is classified as BENIGN. Following criteria are met: BA1 - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 15, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at