chr16-67659894-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001082486.2(ACD):c.242+9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ACD
NM_001082486.2 intron
NM_001082486.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.36
Publications
0 publications found
Genes affected
ACD (HGNC:25070): (ACD shelterin complex subunit and telomerase recruitment factor) This gene encodes a protein that is involved in telomere function. This protein is one of six core proteins in the telosome/shelterin telomeric complex, which functions to maintain telomere length and to protect telomere ends. Through its interaction with other components, this protein plays a key role in the assembly and stabilization of this complex, and it mediates the access of telomerase to the telomere. Multiple transcript variants encoding different isoforms have been found for this gene. This gene, which is also referred to as TPP1, is distinct from the unrelated TPP1 gene on chromosome 11, which encodes tripeptidyl-peptidase I. [provided by RefSeq, Jul 2008]
ACD Gene-Disease associations (from GenCC):
- ACD-related short telomere syndromeInheritance: SD Classification: DEFINITIVE Submitted by: ClinGen
- dyskeratosis congenita, autosomal dominant 6Inheritance: AR, AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P
- hereditary isolated aplastic anemiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Hoyeraal-Hreidarsson syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 16-67659894-G-T is Benign according to our data. Variant chr16-67659894-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2576230.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001082486.2. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1432102Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 708712
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1432102
Hom.:
Cov.:
34
AF XY:
AC XY:
0
AN XY:
708712
African (AFR)
AF:
AC:
0
AN:
33008
American (AMR)
AF:
AC:
0
AN:
43232
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24698
East Asian (EAS)
AF:
AC:
0
AN:
39262
South Asian (SAS)
AF:
AC:
0
AN:
83714
European-Finnish (FIN)
AF:
AC:
0
AN:
47764
Middle Eastern (MID)
AF:
AC:
0
AN:
5672
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1095632
Other (OTH)
AF:
AC:
0
AN:
59120
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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