chr10-88935012-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NR_125373.1(ACTA2-AS1):n.637C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00484 in 569,254 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.014 ( 34 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 8 hom. )
Consequence
ACTA2-AS1
NR_125373.1 non_coding_transcript_exon
NR_125373.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.91
Genes affected
ACTA2-AS1 (HGNC:45169): (ACTA2 antisense RNA 1)
STAMBPL1 (HGNC:24105): (STAM binding protein like 1) Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein K63-linked deubiquitination. Located in membrane. [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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 10-88935012-C-T is Benign according to our data. Variant chr10-88935012-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1198277.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0137 (2081/152054) while in subpopulation AFR AF= 0.0474 (1967/41464). AF 95% confidence interval is 0.0457. There are 34 homozygotes in gnomad4. There are 983 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 34 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTA2-AS1 | NR_125373.1 | n.637C>T | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTA2-AS1 | ENST00000437930.4 | n.678C>T | non_coding_transcript_exon_variant | 3/5 | 2 | ||||
STAMBPL1 | ENST00000371927.7 | c.1254+12576C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0137 AC: 2076AN: 151940Hom.: 34 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
2076
AN:
151940
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:
GnomAD4 exome AF: 0.00162 AC: 675AN: 417200Hom.: 8 Cov.: 6 AF XY: 0.00135 AC XY: 298AN XY: 220130
GnomAD4 exome
AF:
AC:
675
AN:
417200
Hom.:
Cov.:
6
AF XY:
AC XY:
298
AN XY:
220130
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: 0.0137 AC: 2081AN: 152054Hom.: 34 Cov.: 32 AF XY: 0.0132 AC XY: 983AN XY: 74328
GnomAD4 genome
?
AF:
AC:
2081
AN:
152054
Hom.:
Cov.:
32
AF XY:
AC XY:
983
AN XY:
74328
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
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at