rs6456889

Variant names:

• chr6-29043047-T-C
• rs6456889
• ENST00000610326.2:n.176+6829T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000623946.1(OR2W1-AS1):​n.259-1198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,982 control chromosomes in the GnomAD database, including 10,267 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 0.34 (10267 hom., cov: 32)
• Consequence: OR2W1-AS1 ENST00000623946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 16 publications found

Genes affected

OR2W1-AS1 (HGNC:50896): (OR2W1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623946.1. 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
	OR2W1-AS1	NR_125387.1		n.30+6997T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2W1-AS1	ENST00000610326.2	TSL:5	n.176+6829T>C		intron	N/A
	OR2W1-AS1	ENST00000623334.4	TSL:3	n.60+6997T>C		intron	N/A
	OR2W1-AS1	ENST00000623946.1	TSL:2	n.259-1198T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51387 AN: 151864 Hom.: 10247 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.339 AC: 51448 AN: 151982 Hom.: 10267 Cov.: 32 AF XY: 0.341 AC XY: 25301 AN XY: 74272

African (AFR) AF: 0.553 AC: 22921 AN: 41452

American (AMR) AF: 0.289 AC: 4416 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1171 AN: 5180

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4820

European-Finnish (FIN) AF: 0.286 AC: 3019 AN: 10550

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.236 AC: 16001 AN: 67934

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.295 Hom.: 12738

Bravo AF: 0.351

Asia WGS AF: 0.286 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6456889;

hg19: chr6-29010824;