rs6826006

chr4-172763130-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001034845.3(GALNTL6):c.554-46231A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,174 control chromosomes in the GnomAD database, including 255 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 0.044 (255 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.708

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.554-46231A>G		intron_variant		ENST00000506823.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.554-46231A>G		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.503-46231A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0442 AC: 6720 AN: 152054 Hom.: 255 Cov.: 32

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0428

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.0500

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0442 AC: 6721 AN: 152174 Hom.: 255 Cov.: 32 AF XY: 0.0453 AC XY: 3370 AN XY: 74402

Gnomad4 AFR AF: 0.0998

Gnomad4 AMR AF: 0.0427

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.0497

Gnomad4 SAS AF: 0.0889

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0308

Alfa AF: 0.0401 Hom.: 27

Bravo AF: 0.0461

Asia WGS AF: 0.0800 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.8
Dann	Benign	0.34

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

LitVar

Other links and lift over

dbSNP: rs6826006; hg19: chr4-173684281;