rs337997

chr4-172545070-T-Achr4-172545070-T-G

Variant summary

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

The NM_001034845.3(GALNTL6):c.553+196381T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,274 control chromosomes in the GnomAD database, including 996 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 0.11 (996 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.553+196381T>A		intron_variant		ENST00000506823.6
GALNTL6	XM_011531993.3	c.316+196381T>A		intron_variant
GALNTL6	XM_017008243.3	c.553+196381T>A		intron_variant
GALNTL6	XM_017008244.3	c.577+196381T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.553+196381T>A		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.502+196381T>A		intron_variant		1
GALNTL6	ENST00000457021.1	n.546-579T>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16333 AN: 152156 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.107 AC: 16339 AN: 152274 Hom.: 996 Cov.: 32 AF XY: 0.108 AC XY: 8035 AN XY: 74452

Gnomad4 AFR AF: 0.0454

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0999

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.113

Alfa AF: 0.108 Hom.: 108

Bravo AF: 0.110

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.66
Dann	Benign	0.72

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: rs337997; hg19: chr4-173466221;