19-9251064-CTTT-CTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001079935.2(OR7E24):​c.31_32dupTT​(p.Leu12SerfsTer89) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000371 in 1,052,508 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000037 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

OR7E24
NM_001079935.2 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.465
Variant links:
Genes affected
OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) 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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
OR7E24NM_001079935.2 linkc.31_32dupTT p.Leu12SerfsTer89 frameshift_variant Exon 1 of 1 ENST00000456448.3 NP_001073404.1 Q6IFN5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
OR7E24ENST00000456448.3 linkc.31_32dupTT p.Leu12SerfsTer89 frameshift_variant Exon 1 of 1 6 NM_001079935.2 ENSP00000387523.1 Q6IFN5
OR7E24ENST00000641946.1 linkc.30-11_30-10dupTT intron_variant Intron 1 of 1 ENSP00000494223.1 A0A2R8Y4Q1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
147888
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000371
AC:
39
AN:
1052508
Hom.:
0
Cov.:
30
AF XY:
0.0000440
AC XY:
23
AN XY:
523242
show subpopulations
Gnomad4 AFR exome
AF:
0.000332
Gnomad4 AMR exome
AF:
0.0000325
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000805
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000249
Gnomad4 OTH exome
AF:
0.0000921
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
147888
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
71934
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

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: rs201985790; hg19: chr19-9361740; API