Variant 19-14799626-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370485.4(OR7C1):c.511G>A(p.Glu171Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 1,614,044 control chromosomes in the GnomAD database, including 682,648 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.94 ( 66785 hom., cov: 30)

Exomes 𝑓: 0.92 ( 615863 hom. )

Consequence

OR7C1
NM_001370485.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -7.03

Variant links:

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]

OR7C1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.3848052E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR7C1	NM_001370485.4 linkuse as main transcript	c.511G>A	p.Glu171Lys	missense_variant	5/5	ENST00000641666.2
OR7C1	NM_198944.1 linkuse as main transcript	c.511G>A	p.Glu171Lys	missense_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR7C1	ENST00000641666.2 linkuse as main transcript	c.511G>A	p.Glu171Lys	missense_variant	5/5		NM_001370485.4	P1

Frequencies

GnomAD3 genomes

AF:

0.936

AC:

142308

AN:

152036

Hom.:

66725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.983

Gnomad AMI

AF:

0.889

Gnomad AMR

AF:

0.938

Gnomad ASJ

AF:

0.924

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.984

Gnomad FIN

AF:

0.907

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.905

Gnomad OTH

AF:

0.940

GnomAD3 exomes

AF:

0.935

AC:

235213

AN:

251444

Hom.:

110222

AF XY:

0.934

AC XY:

126979

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.984

Gnomad AMR exome

AF:

0.957

Gnomad ASJ exome

AF:

0.918

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.983

Gnomad FIN exome

AF:

0.909

Gnomad NFE exome

AF:

0.906

Gnomad OTH exome

AF:

0.924

GnomAD4 exome

AF:

0.917

AC:

1341185

AN:

1461890

Hom.:

615863

Cov.:

AF XY:

0.919

AC XY:

668103

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.986

Gnomad4 AMR exome

AF:

0.955

Gnomad4 ASJ exome

AF:

0.917

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.983

Gnomad4 FIN exome

AF:

0.906

Gnomad4 NFE exome

AF:

0.906

Gnomad4 OTH exome

AF:

0.926

GnomAD4 genome

AF:

0.936

AC:

142428

AN:

152154

Hom.:

66785

Cov.:

AF XY:

0.938

AC XY:

69770

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.983

Gnomad4 AMR

AF:

0.938

Gnomad4 ASJ

AF:

0.924

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.984

Gnomad4 FIN

AF:

0.907

Gnomad4 NFE

AF:

0.905

Gnomad4 OTH

AF:

0.941

Alfa

AF:

0.914

Hom.:

100326

Bravo

AF:

0.939

TwinsUK

AF:

0.907

AC:

3365

ALSPAC

AF:

0.905

AC:

3487

ESP6500AA

AF:

0.984

AC:

4337

ESP6500EA

AF:

0.910

AC:

7824

ExAC

AF:

0.935

AC:

113544

Asia WGS

AF:

0.989

AC:

3441

AN:

3478

EpiCase

AF:

0.907

EpiControl

AF:

0.906

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.032

DANN

Benign

0.79

DEOGEN2

Benign

0.0037

T;T;T;T

Eigen

Benign

-1.8

Eigen_PC

Benign

-2.0

FATHMM_MKL

Benign

0.0045

LIST_S2

Benign

0.047

.;.;.;T

MetaRNN

Benign

0.0000014

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.61

N;N;N;N

MutationTaster

Benign

1.0

PrimateAI

Benign

0.19

PROVEAN

Benign

-1.5

.;.;.;N

REVEL

Benign

0.019

Sift

Benign

0.20

.;.;.;T

Sift4G

Benign

0.14

.;.;.;T

Polyphen

0.017

B;B;B;B

Vest4

0.041

MPC

0.24

ClinPred

0.012

GERP RS

-7.3

Varity_R

0.073

gMVP

0.14

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over