rs1347706

Positions:

• chr4-172765357-T-A

Variant summary

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

The NM_001034845.3(GALNTL6):​c.554-44004T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,990 control chromosomes in the GnomAD database, including 18,332 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 0.48 (18332 hom., cov: 33)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.554-44004T>A		intron_variant		ENST00000506823.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.554-44004T>A		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.503-44004T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72824 AN: 151872 Hom.: 18293 Cov.: 33

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.480 AC: 72921 AN: 151990 Hom.: 18332 Cov.: 33 AF XY: 0.474 AC XY: 35183 AN XY: 74304

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.471

Alfa AF: 0.455 Hom.: 2036

Bravo AF: 0.497

Asia WGS AF: 0.318 AC: 1110 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.63

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: rs1347706; hg19: chr4-173686508;