4-172668339-G-C

Position:

• chr4-172668339-G-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.554-141022G>C		intron_variant		ENST00000506823.6	NP_001030017.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.554-141022G>C		intron_variant		1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.503-141022G>C		intron_variant		1		ENSP00000423827.1
GALNTL6	ENST00000457021.1	n.2200G>C		non_coding_transcript_exon_variant	6/6	1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95194 AN: 151934 Hom.: 30831 Cov.: 32

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: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.626 AC: 95240 AN: 152052 Hom.: 30840 Cov.: 32 AF XY: 0.637 AC XY: 47353 AN XY: 74330

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.634

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.4
DANN	Benign	0.44

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: rs1347703; hg19: chr4-173589490;