chr19-14793603-G-A

Variant names:

• chr19-14793603-G-A
• rs2190687
• ENST00000642000.1:c.*5571C>T

Variant summary

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

The ENST00000642000.1(OR7C1):​c.*5571C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,018 control chromosomes in the GnomAD database, including 4,837 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 0.23 (4837 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: OR7C1 ENST00000642000.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OR7C1	ENST00000642000.1	c.*5571C>T		3_prime_UTR_variant	Exon 3 of 3			ENSP00000493248.1
OR7C1	ENST00000642030.1	c.*5571C>T		3_prime_UTR_variant	Exon 6 of 6			ENSP00000493026.1
OR7C1	ENST00000601611.6	n.492-1011C>T		intron_variant	Intron 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35420 AN: 151900 Hom.: 4816 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.225

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.233 AC: 35486 AN: 152018 Hom.: 4837 Cov.: 32 AF XY: 0.231 AC XY: 17146 AN XY: 74290

African (AFR) AF: 0.368 AC: 15234 AN: 41438

American (AMR) AF: 0.245 AC: 3737 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5180

South Asian (SAS) AF: 0.149 AC: 717 AN: 4814

European-Finnish (FIN) AF: 0.172 AC: 1822 AN: 10564

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12810 AN: 67962

Other (OTH) AF: 0.223 AC: 471 AN: 2116

Alfa AF: 0.188 Hom.: 3978

Bravo AF: 0.243

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.24
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2190687; hg19: chr19-14904415;