rs6456889

chr6-29043047-T-C

Variant summary

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

The NR_125387.1(OR2W1-AS1):n.30+6997T>C variant causes a intron, non coding transcript 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 NR_125387.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR2W1-AS1	NR_125387.1	n.30+6997T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR2W1-AS1	ENST00000623334.3	n.30+6997T>C		intron_variant, non_coding_transcript_variant		3
OR2W1-AS1	ENST00000623946.1	n.259-1198T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.336

Alfa AF: 0.265 Hom.: 5729

Bravo AF: 0.351

Asia WGS AF: 0.286 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.5
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6456889; hg19: chr6-29010824;