1-15219737-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001136218.2(TMEM51):c.756C>T(p.Pro252Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000804 in 1,612,574 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0022 ( 7 hom., cov: 32)
Exomes 𝑓: 0.00066 ( 11 hom. )
Consequence
TMEM51
NM_001136218.2 synonymous
NM_001136218.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.52
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 1-15219737-C-T is Benign according to our data. Variant chr1-15219737-C-T is described in ClinVar as [Benign]. Clinvar id is 731484.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.52 with no splicing effect.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00219 (334/152334) while in subpopulation AMR AF= 0.0205 (314/15302). AF 95% confidence interval is 0.0187. There are 7 homozygotes in gnomad4. There are 208 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM51 | NM_001136218.2 | c.756C>T | p.Pro252Pro | synonymous_variant | Exon 4 of 4 | ENST00000376008.3 | NP_001129690.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00219 AC: 333AN: 152216Hom.: 7 Cov.: 32
GnomAD3 genomes
AF:
AC:
333
AN:
152216
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: 0.00267 AC: 658AN: 246452Hom.: 7 AF XY: 0.00225 AC XY: 303AN XY: 134398
GnomAD3 exomes
AF:
AC:
658
AN:
246452
Hom.:
AF XY:
AC XY:
303
AN XY:
134398
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: 0.000659 AC: 963AN: 1460240Hom.: 11 Cov.: 32 AF XY: 0.000613 AC XY: 445AN XY: 726250
GnomAD4 exome
AF:
AC:
963
AN:
1460240
Hom.:
Cov.:
32
AF XY:
AC XY:
445
AN XY:
726250
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: 0.00219 AC: 334AN: 152334Hom.: 7 Cov.: 32 AF XY: 0.00279 AC XY: 208AN XY: 74484
GnomAD4 genome
AF:
AC:
334
AN:
152334
Hom.:
Cov.:
32
AF XY:
AC XY:
208
AN XY:
74484
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:
6
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
May 29, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
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