GeneBe

rs55866014

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_201544.4(LGALS8):​c.*2841_*2849delAAAAAAAAA variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00000358 in 1,117,884 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: not found (cov: 0)
Exomes 𝑓: 0.0000036 ( 0 hom. )

Consequence

LGALS8
NM_201544.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.48

Publications

1 publications found
Variant links:
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 2 ACMG points.

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

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
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
LGALS8
NM_201544.4
MANE Select
c.*2841_*2849delAAAAAAAAA
3_prime_UTR
Exon 10 of 10NP_963838.1
HEATR1
NM_018072.6
MANE Select
c.6347-11_6347-3delTTTTTTTTT
splice_region intron
N/ANP_060542.4
LGALS8
NM_006499.5
c.*2841_*2849delAAAAAAAAA
3_prime_UTR
Exon 12 of 12NP_006490.3

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
LGALS8
ENST00000366584.9
TSL:1 MANE Select
c.*2841_*2849delAAAAAAAAA
3_prime_UTR
Exon 10 of 10ENSP00000355543.4
LGALS8
ENST00000450372.6
TSL:1
c.*2841_*2849delAAAAAAAAA
3_prime_UTR
Exon 12 of 12ENSP00000408657.2
HEATR1
ENST00000366582.8
TSL:5 MANE Select
c.6347-11_6347-3delTTTTTTTTT
splice_region intron
N/AENSP00000355541.3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000358
AC:
4
AN:
1117884
Hom.:
0
AF XY:
0.00000360
AC XY:
2
AN XY:
556220
show subpopulations
African (AFR)
AF:
0.000153
AC:
4
AN:
26072
American (AMR)
AF:
0.00
AC:
0
AN:
23784
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19030
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34238
South Asian (SAS)
AF:
0.00
AC:
0
AN:
61164
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
31256
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3894
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
870380
Other (OTH)
AF:
0.00
AC:
0
AN:
48066
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.413
Heterozygous variant carriers
0
1
1
2
2
3
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
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
4.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs55866014; hg19: chr1-236714292; API