rs857859

chr1-158801660-T-Achr1-158801660-T-Cchr1-158801660-T-G

Variant summary

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

The XM_017000325.2(OR6N1):c.-193-29465A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 152,050 control chromosomes in the GnomAD database, including 24,846 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 0.52 (24846 hom., cov: 31)
• Consequence: OR6N1 XM_017000325.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380

Genes affected

OR6N1 (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 (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR6N1	XM_017000325.2	c.-193-29465A>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79679 AN: 151932 Hom.: 24771 Cov.: 31

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.466

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.525 AC: 79822 AN: 152050 Hom.: 24846 Cov.: 31 AF XY: 0.528 AC XY: 39233 AN XY: 74338

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.473

Alfa AF: 0.439 Hom.: 2062

Bravo AF: 0.541

Asia WGS AF: 0.648 AC: 2255 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	6.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs857859; hg19: chr1-158771450;