rs7341211

Variant summary

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

The NM_030883.5(OR2H1):​c.-327+791G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.034 in 152,226 control chromosomes in the GnomAD database, including 213 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.034 ( 213 hom., cov: 32)

Consequence

OR2H1
NM_030883.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0470
Variant links:
Genes affected
OR2H1 (HGNC:8252): (olfactory receptor family 2 subfamily H 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]

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 (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
OR2H1NM_030883.5 linkuse as main transcriptc.-327+791G>A intron_variant ENST00000377133.6 NP_112145.1 Q9GZK4A0A024RCM6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
OR2H1ENST00000377133.6 linkuse as main transcriptc.-327+791G>A intron_variant 6 NM_030883.5 ENSP00000366337.1 Q9GZK4
OR2H1ENST00000377136.5 linkuse as main transcriptc.-323+791G>A intron_variant 6 ENSP00000366340.1 Q9GZK4
OR2H1ENST00000484371.1 linkuse as main transcriptn.122-661G>A intron_variant 6

Frequencies

GnomAD3 genomes
AF:
0.0339
AC:
5162
AN:
152108
Hom.:
212
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.103
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0198
Gnomad ASJ
AF:
0.0222
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00290
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.00616
Gnomad OTH
AF:
0.0364
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0340
AC:
5172
AN:
152226
Hom.:
213
Cov.:
32
AF XY:
0.0325
AC XY:
2419
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.103
Gnomad4 AMR
AF:
0.0197
Gnomad4 ASJ
AF:
0.0222
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00270
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00616
Gnomad4 OTH
AF:
0.0360
Alfa
AF:
0.0220
Hom.:
30
Bravo
AF:
0.0386
Asia WGS
AF:
0.00866
AC:
30
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.9
DANN
Benign
0.38

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.

Other links and lift over

dbSNP: rs7341211; hg19: chr6-29427137; API