rs6518322
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_026961.1(AATBC):n.4369T>C 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 0.573 in 151,958 control chromosomes in the GnomAD database, including 26,971 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.57 ( 26960 hom., cov: 31)
Exomes 𝑓: 0.56 ( 11 hom. )
Consequence
AATBC
NR_026961.1 non_coding_transcript_exon
NR_026961.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.134
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AATBC | NR_026961.1 | n.4369T>C | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AATBC | ENST00000400385.2 | n.4369T>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
AATBC | ENST00000437258.5 | n.703T>C | non_coding_transcript_exon_variant | 2/2 | 1 | ||||
AATBC | ENST00000448247.5 | n.1660T>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.573 AC: 86953AN: 151768Hom.: 26914 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
86953
AN:
151768
Hom.:
Cov.:
31
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: 0.556 AC: 40AN: 72Hom.: 11 Cov.: 0 AF XY: 0.500 AC XY: 14AN XY: 28
GnomAD4 exome
AF:
AC:
40
AN:
72
Hom.:
Cov.:
0
AF XY:
AC XY:
14
AN XY:
28
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.573 AC: 87056AN: 151886Hom.: 26960 Cov.: 31 AF XY: 0.580 AC XY: 43040AN XY: 74242
GnomAD4 genome
?
AF:
AC:
87056
AN:
151886
Hom.:
Cov.:
31
AF XY:
AC XY:
43040
AN XY:
74242
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:
2612
AN:
3478
ClinVar
Not reported inComputational 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