Genetic Variant GALNTL6:c.554-141022G>C (chr4-172668339-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001034845.3(GALNTL6):c.554-141022G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,054 control chromosomes in the GnomAD database, including 30,840 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 0.63 ( 30840 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

GALNTL6
NM_001034845.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.346

Publications

1 publications found

Variant links:

Genes affected

GALNTL6 (HGNC:33844): (polypeptide N-acetylgalactosaminyltransferase like 6) Enables polypeptide N-acetylgalactosaminyltransferase activity. Involved in protein O-linked glycosylation via threonine. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

GALNTL6 links:

ENSG00000303359 (HGNC:):

ENSG00000303359 links:

GALNTL6-AS1 (HGNC:54079): (GALNTL6 antisense RNA 1)

GALNTL6-AS1 links:

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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=-0.72).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001034845.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GALNTL6	NM_001034845.3	MANE Select	c.554-141022G>C	intron	N/A	NP_001030017.2	Q49A17-1
GALNTL6-AS1	NR_125894.1		n.56-4077C>G	intron	N/A
GALNTL6-AS1	NR_125895.1		n.32-4077C>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GALNTL6	ENST00000506823.6	TSL:1 MANE Select	c.554-141022G>C	intron	N/A	ENSP00000423313.1	Q49A17-1
GALNTL6	ENST00000508122.5	TSL:1	c.503-141022G>C	intron	N/A	ENSP00000423827.1	Q49A17-2
GALNTL6	ENST00000457021.1	TSL:1	n.2200G>C	non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.627

AC:

95194

AN:

151934

Hom.:

30831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.489

Gnomad AMI

AF:

0.663

Gnomad AMR

AF:

0.731

Gnomad ASJ

AF:

0.641

Gnomad EAS

AF:

0.984

Gnomad SAS

AF:

0.740

Gnomad FIN

AF:

0.747

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.632

Gnomad OTH

AF:

0.636

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.626

AC:

95240

AN:

152052

Hom.:

30840

Cov.:

AF XY:

0.637

AC XY:

47353

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.489

AC:

20255

AN:

41450

American (AMR)

AF:

0.731

AC:

11175

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.641

AC:

2225

AN:

3472

East Asian (EAS)

AF:

0.984

AC:

5086

AN:

5168

South Asian (SAS)

AF:

0.739

AC:

3568

AN:

4826

European-Finnish (FIN)

AF:

0.747

AC:

7911

AN:

10584

Middle Eastern (MID)

AF:

0.517

AC:

151

AN:

292

European-Non Finnish (NFE)

AF:

0.632

AC:

42929

AN:

67962

Other (OTH)

AF:

0.634

AC:

1337

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1723

3446

5169

6892

8615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.627

Hom.:

3635

Bravo

AF:

0.622

Asia WGS

AF:

0.834

AC:

2897

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

3.4

(source)

DANN

Benign

0.44

PhyloP100

-0.35

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over