19-14829189-T-C

Variant names:

• chr19-14829189-T-C
• rs8101893
• NM_001370485.4:c.-623+5885A>G

Variant summary

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

The NM_001370485.4(OR7C1):​c.-623+5885A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,014 control chromosomes in the GnomAD database, including 6,847 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 0.29 (6847 hom., cov: 32)
• Consequence: OR7C1 NM_001370485.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996
• Publications: 7 publications found

Genes affected

OR7C1 (HGNC:8373): (olfactory receptor family 7 subfamily C member 1) 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]

OR7A5 (HGNC:8368): (olfactory receptor family 7 subfamily A member 5) 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370485.4. 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
	OR7C1	NM_001370485.4	MANE Select	c.-623+5885A>G		intron	N/A	NP_001357414.2
	OR7A5	NM_017506.2	MANE Select	c.-13-935A>G		intron	N/A	NP_059976.1
	OR7A5	NM_001370480.1		c.-248-598A>G		intron	N/A	NP_001357409.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7C1	ENST00000641666.2	MANE Select	c.-623+5885A>G		intron	N/A	ENSP00000493429.1
	OR7A5	ENST00000322301.5	TSL:6 MANE Select	c.-13-935A>G		intron	N/A	ENSP00000316955.3
	OR7C1	ENST00000642000.1		c.-202+5885A>G		intron	N/A	ENSP00000493248.1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44393 AN: 151896 Hom.: 6830 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.292 AC: 44435 AN: 152014 Hom.: 6847 Cov.: 32 AF XY: 0.298 AC XY: 22126 AN XY: 74310

African (AFR) AF: 0.264 AC: 10960 AN: 41494

American (AMR) AF: 0.336 AC: 5137 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3460

East Asian (EAS) AF: 0.556 AC: 2871 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1767 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3664 AN: 10564

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18601 AN: 67934

Other (OTH) AF: 0.267 AC: 563 AN: 2108

Alfa AF: 0.266 Hom.: 4674

Bravo AF: 0.289

Asia WGS AF: 0.471 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.41
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8101893; hg19: chr19-14940001;