Genetic Variant LGALS8:c.*2843_*2849delAAAAAAA (chr1-236550992-TAAAAAAA-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

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

The NM_201544.4(LGALS8):c.*2843_*2849delAAAAAAA variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0000143 in 1,255,680 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: 𝑓 0.000015 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000014 ( 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]

LGALS8 links:

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]

HEATR1 links:

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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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LGALS8	NM_201544.4	MANE Select	c.2843_2849delAAAAAAA	3_prime_UTR	Exon 10 of 10	NP_963838.1
HEATR1	NM_018072.6	MANE Select	c.6347-9_6347-3delTTTTTTT	splice_region intron	N/A	NP_060542.4
LGALS8	NM_006499.5		c.2843_2849delAAAAAAA	3_prime_UTR	Exon 12 of 12	NP_006490.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LGALS8	ENST00000366584.9	TSL:1 MANE Select	c.2843_2849delAAAAAAA	3_prime_UTR	Exon 10 of 10	ENSP00000355543.4
LGALS8	ENST00000450372.6	TSL:1	c.2843_2849delAAAAAAA	3_prime_UTR	Exon 12 of 12	ENSP00000408657.2
HEATR1	ENST00000366582.8	TSL:5 MANE Select	c.6347-9_6347-3delTTTTTTT	splice_region intron	N/A	ENSP00000355541.3

Frequencies

GnomAD3 genomes

AF:

0.0000145

AC:

AN:

137788

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000156

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000143

AC:

AN:

1117892

Hom.:

AF XY:

0.0000144

AC XY:

AN XY:

556230

show subpopulations

African (AFR)

AF:

0.0000383

AC:

AN:

26086

American (AMR)

AF:

0.00

AC:

AN:

23786

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19028

East Asian (EAS)

AF:

0.00

AC:

AN:

34238

South Asian (SAS)

AF:

0.00

AC:

AN:

61164

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31256

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3894

European-Non Finnish (NFE)

AF:

0.0000172

AC:

AN:

870372

Other (OTH)

AF:

0.00

AC:

AN:

48068

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.456

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0000145

AC:

AN:

137788

Hom.:

Cov.:

AF XY:

0.0000304

AC XY:

AN XY:

65728

show subpopulations

African (AFR)

AF:

0.0000265

AC:

AN:

37692

American (AMR)

AF:

0.00

AC:

AN:

13748

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3322

East Asian (EAS)

AF:

0.00

AC:

AN:

4736

South Asian (SAS)

AF:

0.00

AC:

AN:

4208

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6822

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0000156

AC:

AN:

64256

Other (OTH)

AF:

0.00

AC:

AN:

1852

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over