16-66770100-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001136505.2(TERB1):c.1482G>A(p.Pro494Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,552,058 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 (★).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00018 ( 2 hom. )
Consequence
TERB1
NM_001136505.2 synonymous
NM_001136505.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.901
Genes affected
TERB1 (HGNC:26675): (telomere repeat binding bouquet formation protein 1) Predicted to be involved in homologous chromosome pairing at meiosis and meiotic attachment of telomere to nuclear envelope. Predicted to be located in chromosome, telomeric region and nuclear inner membrane. Predicted to colocalize with shelterin complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 16-66770100-C-T is Benign according to our data. Variant chr16-66770100-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388112.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.901 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TERB1 | NM_001136505.2 | c.1482G>A | p.Pro494Pro | synonymous_variant | Exon 14 of 19 | ENST00000433154.6 | NP_001129977.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TERB1 | ENST00000433154.6 | c.1482G>A | p.Pro494Pro | synonymous_variant | Exon 14 of 19 | 5 | NM_001136505.2 | ENSP00000463762.1 | ||
TERB1 | ENST00000558713.6 | c.1482G>A | p.Pro494Pro | synonymous_variant | Exon 13 of 18 | 5 | ENSP00000462883.1 | |||
TERB1 | ENST00000313294.7 | n.1356G>A | non_coding_transcript_exon_variant | Exon 13 of 16 | 5 | ENSP00000464579.1 | ||||
TERB1 | ENST00000561333.1 | n.1713G>A | non_coding_transcript_exon_variant | Exon 14 of 15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152162Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
35
AN:
152162
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000575 AC: 91AN: 158258Hom.: 2 AF XY: 0.000587 AC XY: 49AN XY: 83488
GnomAD3 exomes
AF:
AC:
91
AN:
158258
Hom.:
AF XY:
AC XY:
49
AN XY:
83488
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000184 AC: 257AN: 1399778Hom.: 2 Cov.: 31 AF XY: 0.000191 AC XY: 132AN XY: 690354
GnomAD4 exome
AF:
AC:
257
AN:
1399778
Hom.:
Cov.:
31
AF XY:
AC XY:
132
AN XY:
690354
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000230 AC: 35AN: 152280Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74446
GnomAD4 genome
AF:
AC:
35
AN:
152280
Hom.:
Cov.:
32
AF XY:
AC XY:
17
AN XY:
74446
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
TERB1: BP4, BP7 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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