rs34368910
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_017489.3(TERF1):āc.1258T>Cā(p.Leu420=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00154 in 1,610,046 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0069 ( 8 hom., cov: 32)
Exomes š: 0.00098 ( 12 hom. )
Consequence
TERF1
NM_017489.3 synonymous
NM_017489.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.355
Genes affected
TERF1 (HGNC:11728): (telomeric repeat binding factor 1) This gene encodes a telomere specific protein which is a component of the telomere nucleoprotein complex. This protein is present at telomeres throughout the cell cycle and functions as an inhibitor of telomerase, acting in cis to limit the elongation of individual chromosome ends. The protein structure contains a C-terminal Myb motif, a dimerization domain near its N-terminus and an acidic N-terminus. Multiple transcripts of this gene are alternatively spliced products. [provided by RefSeq, Aug 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
?
Variant 8-73046075-T-C is Benign according to our data. Variant chr8-73046075-T-C is described in ClinVar as [Benign]. Clinvar id is 784130.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.355 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00691 (1052/152302) while in subpopulation AFR AF= 0.0233 (967/41556). AF 95% confidence interval is 0.0221. There are 8 homozygotes in gnomad4. There are 519 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1052 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TERF1 | NM_017489.3 | c.1258T>C | p.Leu420= | synonymous_variant | 10/10 | ENST00000276603.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TERF1 | ENST00000276603.10 | c.1258T>C | p.Leu420= | synonymous_variant | 10/10 | 1 | NM_017489.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00690 AC: 1050AN: 152184Hom.: 8 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1050
AN:
152184
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: 0.00197 AC: 477AN: 242158Hom.: 8 AF XY: 0.00147 AC XY: 193AN XY: 131178
GnomAD3 exomes
AF:
AC:
477
AN:
242158
Hom.:
AF XY:
AC XY:
193
AN XY:
131178
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: 0.000980 AC: 1428AN: 1457744Hom.: 12 Cov.: 30 AF XY: 0.000885 AC XY: 642AN XY: 725140
GnomAD4 exome
AF:
AC:
1428
AN:
1457744
Hom.:
Cov.:
30
AF XY:
AC XY:
642
AN XY:
725140
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: 0.00691 AC: 1052AN: 152302Hom.: 8 Cov.: 32 AF XY: 0.00697 AC XY: 519AN XY: 74470
GnomAD4 genome
?
AF:
AC:
1052
AN:
152302
Hom.:
Cov.:
32
AF XY:
AC XY:
519
AN XY:
74470
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:
Asia WGS
AF:
AC:
9
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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