14-19879052-A-G

Variant names:

• chr14-19879052-A-G
• rs1319956
• NM_001005501.2:c.*1840A>G

Variant summary

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

The NM_001005501.2(OR4K2):​c.*1840A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 148,904 control chromosomes in the GnomAD database, including 5,117 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 (5117 hom., cov: 40)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: OR4K2 NM_001005501.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 4 publications found

Genes affected

OR4K2 (HGNC:14728): (olfactory receptor family 4 subfamily K member 2) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005501.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR4K2	NM_001005501.2	MANE Select	c.*1840A>G		3_prime_UTR	Exon 2 of 2	NP_001005501.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR4K2	ENST00000641885.1	MANE Select	c.*1840A>G		3_prime_UTR	Exon 2 of 2	ENSP00000493007.1
	OR4K2	ENST00000641522.1		n.1244A>G		non_coding_transcript_exon	Exon 3 of 3
	OR4K2	ENST00000641785.1		n.1244A>G		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.345 AC: 51278 AN: 148764 Hom.: 5096 Cov.: 40

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.375 AC: 9 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.375 AC XY: 9 AN XY: 24

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.389 AC: 7 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.345 AC: 51343 AN: 148880 Hom.: 5117 Cov.: 40 AF XY: 0.348 AC XY: 25345 AN XY: 72766

African (AFR) AF: 0.393 AC: 16095 AN: 40916

American (AMR) AF: 0.438 AC: 6568 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 949 AN: 3312

East Asian (EAS) AF: 0.616 AC: 3147 AN: 5112

South Asian (SAS) AF: 0.375 AC: 1767 AN: 4708

European-Finnish (FIN) AF: 0.275 AC: 2832 AN: 10316

Middle Eastern (MID) AF: 0.349 AC: 95 AN: 272

European-Non Finnish (NFE) AF: 0.284 AC: 18842 AN: 66302

Other (OTH) AF: 0.361 AC: 742 AN: 2056

Alfa AF: 0.317 Hom.: 430

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1319956; hg19: chr14-20347211;