4-99089122-C-G
Position:
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