6-28053042-C-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

Genes affected

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

OR2B8 (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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660873.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2B8	NR_174096.1		n.*186G>C		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZSCAN16-AS1	ENST00000660873.1		n.188+7336G>C		intron	N/A
	ZSCAN16-AS1	ENST00000716089.1		n.223+7336G>C		intron	N/A
	ZSCAN16-AS1	ENST00000716090.1		n.310+7336G>C		intron	N/A

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

African (AFR) AF: 0.358 AC: 14782 AN: 41252

American (AMR) AF: 0.259 AC: 3931 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3464

East Asian (EAS) AF: 0.187 AC: 965 AN: 5152

South Asian (SAS) AF: 0.170 AC: 816 AN: 4798

European-Finnish (FIN) AF: 0.148 AC: 1559 AN: 10504

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14831 AN: 67832

Other (OTH) AF: 0.243 AC: 511 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.28
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs172166; hg19: chr6-28020820;