rs1370576

chr4-172744108-G-A

Variant summary

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

The NM_001034845.3(GALNTL6):c.554-65253G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 149,964 control chromosomes in the GnomAD database, including 10,824 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 0.36 (10824 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.554-65253G>A		intron_variant		ENST00000506823.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.554-65253G>A		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.503-65253G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 54446 AN: 149842 Hom.: 10804 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0680

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.363 AC: 54507 AN: 149964 Hom.: 10824 Cov.: 32 AF XY: 0.355 AC XY: 25982 AN XY: 73092

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.0680

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.359

Alfa AF: 0.341 Hom.: 1155

Bravo AF: 0.367

Asia WGS AF: 0.236 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.2
Dann	Benign	0.66

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: rs1370576; hg19: chr4-173665259;