rs15574
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025261.3(LY6G6C):c.*376C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 291,228 control chromosomes in the GnomAD database, including 13,210 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 0.32 ( 8723 hom., cov: 30)
Exomes 𝑓: 0.24 ( 4487 hom. )
Consequence
LY6G6C
NM_025261.3 3_prime_UTR
NM_025261.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.147
Publications
29 publications found
Genes affected
LY6G6C (HGNC:13936): (lymphocyte antigen 6 family member G6C) LY6G6C belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).[supplied by OMIM, Mar 2008]
MPIG6B (HGNC:13937): (megakaryocyte and platelet inhibitory receptor G6b) This gene is a member of the immunoglobulin (Ig) superfamily and is located in the major histocompatibility complex (MHC) class III region. The protein encoded by this gene is a glycosylated, plasma membrane-bound cell surface receptor, but soluble isoforms encoded by some transcript variants have been found in the endoplasmic reticulum and Golgi before being secreted. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
MPIG6B Gene-Disease associations (from GenCC):
- thrombocytopenia, anemia, and myelofibrosisInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LY6G6C | NM_025261.3 | c.*376C>T | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000375819.3 | NP_079537.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LY6G6C | ENST00000375819.3 | c.*376C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_025261.3 | ENSP00000364978.2 | |||
LY6G6C | ENST00000495859.1 | c.*376C>T | 3_prime_UTR_variant | Exon 4 of 4 | 1 | ENSP00000433207.1 | ||||
MPIG6B | ENST00000460663.5 | n.90+37G>A | intron_variant | Intron 1 of 6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.319 AC: 48461AN: 151686Hom.: 8704 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
48461
AN:
151686
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.236 AC: 32899AN: 139424Hom.: 4487 Cov.: 0 AF XY: 0.233 AC XY: 16257AN XY: 69910 show subpopulations
GnomAD4 exome
AF:
AC:
32899
AN:
139424
Hom.:
Cov.:
0
AF XY:
AC XY:
16257
AN XY:
69910
show subpopulations
African (AFR)
AF:
AC:
2218
AN:
5010
American (AMR)
AF:
AC:
1919
AN:
6190
Ashkenazi Jewish (ASJ)
AF:
AC:
1420
AN:
5676
East Asian (EAS)
AF:
AC:
3784
AN:
12784
South Asian (SAS)
AF:
AC:
666
AN:
3008
European-Finnish (FIN)
AF:
AC:
2848
AN:
7856
Middle Eastern (MID)
AF:
AC:
162
AN:
734
European-Non Finnish (NFE)
AF:
AC:
17559
AN:
88548
Other (OTH)
AF:
AC:
2323
AN:
9618
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1169
2338
3506
4675
5844
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
176
352
528
704
880
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.320 AC: 48533AN: 151804Hom.: 8723 Cov.: 30 AF XY: 0.326 AC XY: 24223AN XY: 74194 show subpopulations
GnomAD4 genome
AF:
AC:
48533
AN:
151804
Hom.:
Cov.:
30
AF XY:
AC XY:
24223
AN XY:
74194
show subpopulations
African (AFR)
AF:
AC:
19786
AN:
41346
American (AMR)
AF:
AC:
5188
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
896
AN:
3458
East Asian (EAS)
AF:
AC:
1244
AN:
5172
South Asian (SAS)
AF:
AC:
1392
AN:
4800
European-Finnish (FIN)
AF:
AC:
4161
AN:
10518
Middle Eastern (MID)
AF:
AC:
86
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14923
AN:
67924
Other (OTH)
AF:
AC:
674
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1569
3138
4706
6275
7844
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
458
916
1374
1832
2290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1051
AN:
3478
ClinVar
Not reported inComputational 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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