17-3197642-AATCTGCTCATC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_012352.3(OR1A2):​c.129_139delGCTCATCATCT​(p.Leu44GlyfsTer5) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00148 in 1,608,252 control chromosomes in the GnomAD database, including 32 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0076 ( 15 hom., cov: 32)
Exomes 𝑓: 0.00084 ( 17 hom. )

Consequence

OR1A2
NM_012352.3 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.62
Variant links:
Genes affected
OR1A2 (HGNC:8180): (olfactory receptor family 1 subfamily A member 2) 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 -10 ACMG points.

BP6
Variant 17-3197642-AATCTGCTCATC-A is Benign according to our data. Variant chr17-3197642-AATCTGCTCATC-A is described in ClinVar as [Benign]. Clinvar id is 777087.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00763 (1162/152212) while in subpopulation AFR AF= 0.0268 (1111/41530). AF 95% confidence interval is 0.0254. There are 15 homozygotes in gnomad4. There are 519 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR1A2NM_012352.3 linkc.129_139delGCTCATCATCT p.Leu44GlyfsTer5 frameshift_variant Exon 1 of 1 ENST00000381951.1 NP_036484.1 Q9Y585A0A126GVH4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR1A2ENST00000381951.1 linkc.129_139delGCTCATCATCT p.Leu44GlyfsTer5 frameshift_variant Exon 1 of 1 6 NM_012352.3 ENSP00000371377.1 Q9Y585

Frequencies

GnomAD3 genomes
AF:
0.00761
AC:
1158
AN:
152094
Hom.:
15
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0267
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00223
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00623
GnomAD3 exomes
AF:
0.00203
AC:
494
AN:
243578
Hom.:
6
AF XY:
0.00141
AC XY:
185
AN XY:
131546
show subpopulations
Gnomad AFR exome
AF:
0.0282
Gnomad AMR exome
AF:
0.000906
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000346
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000542
Gnomad OTH exome
AF:
0.000510
GnomAD4 exome
AF:
0.000837
AC:
1219
AN:
1456040
Hom.:
17
AF XY:
0.000703
AC XY:
509
AN XY:
724188
show subpopulations
Gnomad4 AFR exome
AF:
0.0309
Gnomad4 AMR exome
AF:
0.00117
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000824
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000342
Gnomad4 OTH exome
AF:
0.00150
GnomAD4 genome
AF:
0.00763
AC:
1162
AN:
152212
Hom.:
15
Cov.:
32
AF XY:
0.00697
AC XY:
519
AN XY:
74424
show subpopulations
Gnomad4 AFR
AF:
0.0268
Gnomad4 AMR
AF:
0.00222
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00616
Alfa
AF:
0.00103
Hom.:
1
Bravo
AF:
0.00918
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

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

Submissions by phenotype

not provided Benign:1
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs146311669; hg19: chr17-3100936; API