Menu
GeneBe

19-9213914-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001005191.3(OR7D4):c.924C>T(p.Ala308=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00279 in 1,613,456 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.014 ( 58 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 44 hom. )

Consequence

OR7D4
NM_001005191.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0790
Variant links:
Genes affected
OR7D4 (HGNC:8380): (olfactory receptor family 7 subfamily D member 4) 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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-9213914-G-A is Benign according to our data. Variant chr19-9213914-G-A is described in ClinVar as [Benign]. Clinvar id is 777412.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.079 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0138 (2093/152180) while in subpopulation AFR AF= 0.0474 (1966/41506). AF 95% confidence interval is 0.0456. There are 58 homozygotes in gnomad4. There are 954 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 58 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OR7D4NM_001005191.3 linkuse as main transcriptc.924C>T p.Ala308= synonymous_variant 2/2 ENST00000641669.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OR7D4ENST00000641669.1 linkuse as main transcriptc.924C>T p.Ala308= synonymous_variant 2/2 NM_001005191.3 P1
OR7D4ENST00000308682.3 linkuse as main transcriptc.924C>T p.Ala308= synonymous_variant 1/1 P1
OR7D4ENST00000641244.1 linkuse as main transcriptc.924C>T p.Ala308= synonymous_variant 2/2 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0137
AC:
2086
AN:
152062
Hom.:
58
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0473
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00328
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.000471
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000529
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00420
AC:
1054
AN:
250754
Hom.:
31
AF XY:
0.00305
AC XY:
414
AN XY:
135576
show subpopulations
Gnomad AFR exome
AF:
0.0529
Gnomad AMR exome
AF:
0.00301
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000425
Gnomad FIN exome
AF:
0.000232
Gnomad NFE exome
AF:
0.000574
Gnomad OTH exome
AF:
0.00164
GnomAD4 exome
AF:
0.00165
AC:
2411
AN:
1461276
Hom.:
44
Cov.:
31
AF XY:
0.00141
AC XY:
1024
AN XY:
727002
show subpopulations
Gnomad4 AFR exome
AF:
0.0473
Gnomad4 AMR exome
AF:
0.00313
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000301
Gnomad4 FIN exome
AF:
0.000393
Gnomad4 NFE exome
AF:
0.000332
Gnomad4 OTH exome
AF:
0.00409
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0138
AC:
2093
AN:
152180
Hom.:
58
Cov.:
32
AF XY:
0.0128
AC XY:
954
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.0474
Gnomad4 AMR
AF:
0.00327
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00125
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.000529
Gnomad4 OTH
AF:
0.0132
Alfa
AF:
0.00614
Hom.:
12
Bravo
AF:
0.0157
Asia WGS
AF:
0.00433
AC:
15
AN:
3478
EpiCase
AF:
0.000600
EpiControl
AF:
0.000356

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMay 18, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
6.5
Dann
Benign
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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.

Other links and lift over

dbSNP: rs10419202; hg19: chr19-9324590; API