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GeneBe

16-3328977-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_047434179.1(OR2C1):c.-44+5964T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 150,694 control chromosomes in the GnomAD database, including 39,890 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 0.73 ( 39890 hom., cov: 28)

Consequence

OR2C1
XM_047434179.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.78
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR2C1XM_047434179.1 linkuse as main transcriptc.-44+5964T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.727
AC:
109464
AN:
150576
Hom.:
39886
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.643
Gnomad AMI
AF:
0.827
Gnomad AMR
AF:
0.732
Gnomad ASJ
AF:
0.743
Gnomad EAS
AF:
0.657
Gnomad SAS
AF:
0.835
Gnomad FIN
AF:
0.792
Gnomad MID
AF:
0.674
Gnomad NFE
AF:
0.762
Gnomad OTH
AF:
0.710
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.727
AC:
109503
AN:
150694
Hom.:
39890
Cov.:
28
AF XY:
0.731
AC XY:
53790
AN XY:
73544
show subpopulations
Gnomad4 AFR
AF:
0.643
Gnomad4 AMR
AF:
0.731
Gnomad4 ASJ
AF:
0.743
Gnomad4 EAS
AF:
0.657
Gnomad4 SAS
AF:
0.836
Gnomad4 FIN
AF:
0.792
Gnomad4 NFE
AF:
0.762
Gnomad4 OTH
AF:
0.711
Alfa
AF:
0.693
Hom.:
2127
Bravo
AF:
0.712
Asia WGS
AF:
0.702
AC:
2441
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.83
Dann
Benign
0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs250470; hg19: chr16-3378977; API