Variant chr1-248349465-G-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_001001918.1(OR14C36):c.691G>T(p.Asp231Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,613,194 control chromosomes in the GnomAD database, including 242,214 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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 0.50 ( 19768 hom., cov: 31)

Exomes 𝑓: 0.55 ( 222446 hom. )

Consequence

OR14C36
NM_001001918.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.121

Variant links:

Genes affected

OR14C36 (HGNC:15026): (olfactory receptor family 14 subfamily C member 36) 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]

OR14C36 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.3116002E-4).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OR14C36	NM_001001918.1 linkuse as main transcript	c.691G>T	p.Asp231Tyr	missense_variant	1/1	ENST00000317861.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OR14C36	ENST00000317861.1 linkuse as main transcript	c.691G>T	p.Asp231Tyr	missense_variant	1/1		NM_001001918.1	P1

Frequencies

GnomAD3 genomes

AF:

0.505

AC:

76550

AN:

151708

Hom.:

19760

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.492

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.565

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.519

GnomAD3 exomes

AF:

0.525

AC:

131364

AN:

250396

Hom.:

34857

AF XY:

0.533

AC XY:

72145

AN XY:

135326

show subpopulations

Gnomad AFR exome

AF:

0.393

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.546

Gnomad EAS exome

AF:

0.422

Gnomad SAS exome

AF:

0.526

Gnomad FIN exome

AF:

0.562

Gnomad NFE exome

AF:

0.567

Gnomad OTH exome

AF:

0.551

GnomAD4 exome

AF:

0.550

AC:

803694

AN:

1461368

Hom.:

222446

Cov.:

AF XY:

0.550

AC XY:

399768

AN XY:

727004

show subpopulations

Gnomad4 AFR exome

AF:

0.400

Gnomad4 AMR exome

AF:

0.469

Gnomad4 ASJ exome

AF:

0.546

Gnomad4 EAS exome

AF:

0.428

Gnomad4 SAS exome

AF:

0.530

Gnomad4 FIN exome

AF:

0.566

Gnomad4 NFE exome

AF:

0.563

Gnomad4 OTH exome

AF:

0.545

GnomAD4 genome

AF:

0.505

AC:

76597

AN:

151826

Hom.:

19768

Cov.:

AF XY:

0.505

AC XY:

37508

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.491

Gnomad4 ASJ

AF:

0.544

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.540

Gnomad4 FIN

AF:

0.565

Gnomad4 NFE

AF:

0.559

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.545

Hom.:

35724

Bravo

AF:

0.495

TwinsUK

AF:

0.556

AC:

2060

ALSPAC

AF:

0.564

AC:

2175

ESP6500AA

AF:

0.401

AC:

1768

ESP6500EA

AF:

0.569

AC:

4894

ExAC

AF:

0.526

AC:

63877

Asia WGS

AF:

0.479

AC:

1662

AN:

3478

EpiCase

AF:

0.558

EpiControl

AF:

0.566

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0085

Eigen

Benign

-0.24

Eigen_PC

Benign

-0.44

FATHMM_MKL

Benign

0.033

LIST_S2

Benign

0.37

MetaRNN

Benign

0.00013

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.9

MutationTaster

Benign

1.0

PrimateAI

Benign

0.24

PROVEAN

Uncertain

-3.6

REVEL

Benign

0.082

Sift

Uncertain

0.0080

Sift4G

Uncertain

0.0030

Polyphen

1.0

Vest4

0.079

MPC

0.70

ClinPred

0.022

GERP RS

1.6

Varity_R

0.68

gMVP

0.23

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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