rs172166

Variant names:

• chr6-28053042-C-G
• rs172166
• ENST00000660873.1:n.188+7336G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-28053042-C-G
• chr6-28053042-C-T

Variant summary

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

The ENST00000660873.1(ZSCAN16-AS1):​n.188+7336G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,506 control chromosomes in the GnomAD database, including 5,456 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 0.25 (5456 hom., cov: 31)
• Consequence: ZSCAN16-AS1 ENST00000660873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

Genes affected

ZSCAN16-AS1 (HGNC:48982): (ZSCAN16 antisense RNA 1)

OR2B8P (HGNC:13968): (olfactory receptor family 2 subfamily B member 8 pseudogene) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR2B8P	NR_174096.1	n.*186G>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN16-AS1	ENST00000660873.1	n.188+7336G>C		intron_variant	Intron 2 of 3
OR2B8P	ENST00000432841.1	c.*186G>C		downstream_gene_variant		6		ENSP00000501996.1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38310 AN: 151388 Hom.: 5446 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.253 AC: 38354 AN: 151506 Hom.: 5456 Cov.: 31 AF XY: 0.246 AC XY: 18234 AN XY: 74044

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.243

Alfa AF: 0.221 Hom.: 550

Bravo AF: 0.269

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs172166; hg19: chr6-28020820;