rs17216887
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_037884.1(LOC100507053):n.266C>G 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 0.0324 in 189,386 control chromosomes in the GnomAD database, including 167 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 0.032 ( 129 hom., cov: 32)
Exomes 𝑓: 0.034 ( 38 hom. )
Consequence
LOC100507053
NR_037884.1 non_coding_transcript_exon
NR_037884.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.64
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=-0.8).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.032 (4880/152304) while in subpopulation NFE AF= 0.0508 (3458/68024). AF 95% confidence interval is 0.0494. There are 129 homozygotes in gnomad4. There are 2355 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 129 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC100507053 | NR_037884.1 | n.266C>G | non_coding_transcript_exon_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000500358.6 | n.266C>G | non_coding_transcript_exon_variant | 1/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0321 AC: 4880AN: 152186Hom.: 129 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
4880
AN:
152186
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: 0.0339 AC: 1258AN: 37082Hom.: 38 Cov.: 0 AF XY: 0.0328 AC XY: 636AN XY: 19394
GnomAD4 exome
AF:
AC:
1258
AN:
37082
Hom.:
Cov.:
0
AF XY:
AC XY:
636
AN XY:
19394
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: 0.0320 AC: 4880AN: 152304Hom.: 129 Cov.: 32 AF XY: 0.0316 AC XY: 2355AN XY: 74476
GnomAD4 genome
?
AF:
AC:
4880
AN:
152304
Hom.:
Cov.:
32
AF XY:
AC XY:
2355
AN XY:
74476
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:
22
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