rs2880332

Positions:

• chr15-22040734-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000639059.1(OR4M2-OT1):​c.-787-3703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 0)
• Consequence: OR4M2-OT1 ENST00000639059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

Genes affected

OR4M2-OT1 (HGNC:56199): (OR4M2 overlapping transcript 1)

ENSG00000284500 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OR4M2-OT1	NR_110480.1	n.434+9714T>C		intron_variant
OR4M2-OT1	NR_110481.1	n.166+9714T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OR4M2-OT1	ENST00000639059.1	c.-787-3703T>C		intron_variant		2		ENSP00000493899.1
ENSG00000284500	ENST00000640156.1	n.166+9714T>C		intron_variant		5
ENSG00000284500	ENST00000640881.1	n.434+9714T>C		intron_variant		2

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

Alfa AF: 0.293 Hom.: 44

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
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: rs2880332; hg19: chr15-22328685; COSMIC: COSV73574141; COSMIC: COSV73574141;