16-66770100-C-T

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.901
Variant links:
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
TERB1NM_001136505.2 linkc.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
TERB1ENST00000433154.6 linkc.1482G>A p.Pro494Pro synonymous_variant Exon 14 of 19 5 NM_001136505.2 ENSP00000463762.1 Q8NA31-1
TERB1ENST00000558713.6 linkc.1482G>A p.Pro494Pro synonymous_variant Exon 13 of 18 5 ENSP00000462883.1 Q8NA31-1
TERB1ENST00000313294.7 linkn.1356G>A non_coding_transcript_exon_variant Exon 13 of 16 5 ENSP00000464579.1 Q8NA31-3
TERB1ENST00000561333.1 linkn.1713G>A non_coding_transcript_exon_variant Exon 14 of 15 2

Frequencies

GnomAD3 genomes
AF:
0.000230
AC:
35
AN:
152162
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000197
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00366
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000162
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000575
AC:
91
AN:
158258
Hom.:
2
AF XY:
0.000587
AC XY:
49
AN XY:
83488
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000404
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00624
Gnomad SAS exome
AF:
0.000483
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000130
Gnomad OTH exome
AF:
0.000667
GnomAD4 exome
AF:
0.000184
AC:
257
AN:
1399778
Hom.:
2
Cov.:
31
AF XY:
0.000191
AC XY:
132
AN XY:
690354
show subpopulations
Gnomad4 AFR exome
AF:
0.0000316
Gnomad4 AMR exome
AF:
0.0000840
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00255
Gnomad4 SAS exome
AF:
0.000316
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000992
Gnomad4 OTH exome
AF:
0.000310
GnomAD4 genome
AF:
0.000230
AC:
35
AN:
152280
Hom.:
0
Cov.:
32
AF XY:
0.000228
AC XY:
17
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00367
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000162
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000246
Hom.:
0
Bravo
AF:
0.000348

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
2.3
DANN
Benign
0.41

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs144236917; hg19: chr16-66804003; COSMIC: COSV57609916; API