6-28046819-C-T

Position:

• chr6-28046819-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000429302.1(OR2B7P):​n.386C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.239 in 163,212 control chromosomes in the GnomAD database, including 5,298 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 (5264 hom., cov: 31)
  • Exomes 𝑓: 0.072 (34 hom.)
• Consequence: OR2B7P ENST00000429302.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.96

Genes affected

OR2B7P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• 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/exons	MANE	Protein	UniProt
OR2B7P		n.28046819C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR2B7P	ENST00000429302.1	n.386C>T		non_coding_transcript_exon_variant	1/1	6
ZSCAN16-AS1	ENST00000660873.1	n.188+13559G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38104 AN: 151848 Hom.: 5254 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.0722 AC: 812 AN: 11246 Hom.: 34 Cov.: 0 AF XY: 0.0767 AC XY: 408 AN XY: 5320

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.0952

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0556

Gnomad4 SAS exome AF: 0.0455

Gnomad4 FIN exome AF: 0.0700

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.0942

GnomAD4 genome AF: 0.251 AC: 38147 AN: 151966 Hom.: 5264 Cov.: 31 AF XY: 0.244 AC XY: 18093 AN XY: 74272

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.239

Alfa AF: 0.220 Hom.: 5035

Bravo AF: 0.267

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	4.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs149900; hg19: chr6-28014597;