16-3328977-T-C

Position:

• chr16-3328977-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

OR2C1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: 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	Protein	UniProt
OR2C1	XM_047434179.1	c.-44+5964T>C		intron_variant			XP_047290135.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.727 AC: 109464 AN: 150576 Hom.: 39886 Cov.: 28

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 AF: 0.727 AC: 109503 AN: 150694 Hom.: 39890 Cov.: 28 AF XY: 0.731 AC XY: 53790 AN XY: 73544

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

Other links and lift over

dbSNP: rs250470; hg19: chr16-3378977;