chr11-5402663-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001005567.3(OR51B5):c.-359-55753G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 471,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
OR51B5
NM_001005567.3 intron
NM_001005567.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.403
Publications
1 publications found
Genes affected
HBE1 (HGNC:4830): (hemoglobin subunit epsilon 1) The epsilon globin gene (HBE) is normally expressed in the embryonic yolk sac: two epsilon chains together with two zeta chains (an alpha-like globin) constitute the embryonic hemoglobin Hb Gower I; two epsilon chains together with two alpha chains form the embryonic Hb Gower II. Both of these embryonic hemoglobins are normally supplanted by fetal, and later, adult hemoglobin. The five beta-like globin genes are found within a 45 kb cluster on chromosome 11 in the following order: 5'-epsilon - G-gamma - A-gamma - delta - beta-3' [provided by RefSeq, Jul 2008]
ENSG00000239920 (HGNC:):
OR51B5 (HGNC:19599): (olfactory receptor family 51 subfamily B member 5) 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]
HBG2 (HGNC:4832): (hemoglobin subunit gamma 2) The gamma globin genes (HBG1 and HBG2) are normally expressed in the fetal liver, spleen and bone marrow. Two gamma chains together with two alpha chains constitute fetal hemoglobin (HbF) which is normally replaced by adult hemoglobin (HbA) at birth. In some beta-thalassemias and related conditions, gamma chain production continues into adulthood. The two types of gamma chains differ at residue 136 where glycine is found in the G-gamma product (HBG2) and alanine is found in the A-gamma product (HBG1). The former is predominant at birth. The order of the genes in the beta-globin cluster is: 5'- epsilon -- gamma-G -- gamma-A -- delta -- beta--3'. [provided by RefSeq, Jul 2008]
OR51J1 (HGNC:14856): (olfactory receptor family 51 subfamily J 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 11-5402663-C-T is Benign according to our data. Variant chr11-5402663-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2641538.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001005567.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| HBE1 | TSL:1 | c.-267+102906G>A | intron | N/A | ENSP00000292896.2 | P02100 | |||
| HBE1 | TSL:1 | c.-310+102906G>A | intron | N/A | ENSP00000369586.1 | P02100 | |||
| ENSG00000239920 | TSL:5 | n.*740-56764G>A | intron | N/A | ENSP00000369609.3 | A0A2U3TZJ3 |
Frequencies
GnomAD3 genomes 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
6
AN:
152204
Hom.:
Cov.:
33
Gnomad AFR
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000134 AC: 2AN: 149734 AF XY: 0.0000248 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
149734
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000251 AC: 8AN: 318988Hom.: 0 Cov.: 0 AF XY: 0.0000333 AC XY: 6AN XY: 180198 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
318988
Hom.:
Cov.:
0
AF XY:
AC XY:
6
AN XY:
180198
show subpopulations
African (AFR)
AF:
AC:
0
AN:
8632
American (AMR)
AF:
AC:
0
AN:
27286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10790
East Asian (EAS)
AF:
AC:
0
AN:
9214
South Asian (SAS)
AF:
AC:
0
AN:
59742
European-Finnish (FIN)
AF:
AC:
0
AN:
27106
Middle Eastern (MID)
AF:
AC:
0
AN:
2786
European-Non Finnish (NFE)
AF:
AC:
8
AN:
159064
Other (OTH)
AF:
AC:
0
AN:
14368
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
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0.60
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0.95
Allele balance
GnomAD4 genome 0.0000394 AC: 6AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74348 show subpopulations
GnomAD4 genome
AF:
AC:
6
AN:
152204
Hom.:
Cov.:
33
AF XY:
AC XY:
3
AN XY:
74348
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41454
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10616
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
6
AN:
68040
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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