rs2394514

Variant names:

• chr6-29055437-T-C
• rs2394514
• ENST00000610326.2:n.177-8493T>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.366-8493T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 151,816 control chromosomes in the GnomAD database, including 3,277 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 0.18 (3277 hom., cov: 32)
• Consequence: OR2W1-AS1 ENST00000623946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 5 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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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.31-8493T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR2W1-AS1	ENST00000610326.2	TSL:5	n.177-8493T>C		intron	N/A
	OR2W1-AS1	ENST00000623334.4	TSL:3	n.61-8493T>C		intron	N/A
	OR2W1-AS1	ENST00000623946.1	TSL:2	n.366-8493T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27186 AN: 151698 Hom.: 3269 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.179 AC: 27235 AN: 151816 Hom.: 3277 Cov.: 32 AF XY: 0.178 AC XY: 13193 AN XY: 74266

African (AFR) AF: 0.340 AC: 14112 AN: 41450

American (AMR) AF: 0.153 AC: 2330 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 556 AN: 3456

East Asian (EAS) AF: 0.105 AC: 546 AN: 5182

South Asian (SAS) AF: 0.120 AC: 580 AN: 4814

European-Finnish (FIN) AF: 0.110 AC: 1168 AN: 10624

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7507 AN: 67734

Other (OTH) AF: 0.176 AC: 373 AN: 2114

Alfa AF: 0.173 Hom.: 2067

Bravo AF: 0.195

Asia WGS AF: 0.111 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.2
DANN	Benign	0.90
PhyloP100		0.21

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: rs2394514;

hg19: chr6-29023214;