1-236550992-TAAAAAAAAA-TAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_201544.4(LGALS8):c.*2844_*2849dupAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000073 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
LGALS8
NM_201544.4 3_prime_UTR
NM_201544.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.486
Publications
1 publications found
Genes affected
LGALS8 (HGNC:6569): (galectin 8) This gene encodes a member of the galectin family. Galectins are beta-galactoside-binding animal lectins with conserved carbohydrate recognition domains. The galectins have been implicated in many essential functions including development, differentiation, cell-cell adhesion, cell-matrix interaction, growth regulation, apoptosis, and RNA splicing. This gene is widely expressed in tumoral tissues and seems to be involved in integrin-like cell interactions. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
HEATR1 (HGNC:25517): (HEAT repeat containing 1) Enables RNA binding activity. Involved in positive regulation of rRNA processing and positive regulation of transcription by RNA polymerase I. Located in fibrillar center and mitochondrion. Implicated in pancreatic ductal carcinoma. Biomarker of glioblastoma. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_201544.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LGALS8 | NM_201544.4 | MANE Select | c.*2844_*2849dupAAAAAA | 3_prime_UTR | Exon 10 of 10 | NP_963838.1 | |||
| HEATR1 | NM_018072.6 | MANE Select | c.6347-8_6347-3dupTTTTTT | splice_region intron | N/A | NP_060542.4 | |||
| LGALS8 | NM_006499.5 | c.*2844_*2849dupAAAAAA | 3_prime_UTR | Exon 12 of 12 | NP_006490.3 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LGALS8 | ENST00000366584.9 | TSL:1 MANE Select | c.*2844_*2849dupAAAAAA | 3_prime_UTR | Exon 10 of 10 | ENSP00000355543.4 | |||
| LGALS8 | ENST00000450372.6 | TSL:1 | c.*2844_*2849dupAAAAAA | 3_prime_UTR | Exon 12 of 12 | ENSP00000408657.2 | |||
| HEATR1 | ENST00000366582.8 | TSL:5 MANE Select | c.6347-8_6347-3dupTTTTTT | splice_region intron | N/A | ENSP00000355541.3 |
Frequencies
GnomAD3 genomes 0.00000726 AC: 1AN: 137786Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
137786
Hom.:
Cov.:
0
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: 0.0000152 AC: 17AN: 1117870Hom.: 0 Cov.: 18 AF XY: 0.0000144 AC XY: 8AN XY: 556212 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
17
AN:
1117870
Hom.:
Cov.:
18
AF XY:
AC XY:
8
AN XY:
556212
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
2
AN:
26092
American (AMR)
AF:
AC:
0
AN:
23786
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19030
East Asian (EAS)
AF:
AC:
0
AN:
34238
South Asian (SAS)
AF:
AC:
2
AN:
61164
European-Finnish (FIN)
AF:
AC:
0
AN:
31256
Middle Eastern (MID)
AF:
AC:
1
AN:
3894
European-Non Finnish (NFE)
AF:
AC:
12
AN:
870342
Other (OTH)
AF:
AC:
0
AN:
48068
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00224718), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.396
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
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>80
Age
GnomAD4 genome 0.00000726 AC: 1AN: 137786Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 65726 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
137786
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
65726
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
37692
American (AMR)
AF:
AC:
0
AN:
13746
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3322
East Asian (EAS)
AF:
AC:
0
AN:
4736
South Asian (SAS)
AF:
AC:
0
AN:
4208
European-Finnish (FIN)
AF:
AC:
0
AN:
6822
Middle Eastern (MID)
AF:
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
AC:
1
AN:
64256
Other (OTH)
AF:
AC:
0
AN:
1852
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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