4-172060392-C-T

Position:

• chr4-172060392-C-T

Variant summary

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

The NM_001034845.3(GALNTL6):​c.139-169264C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,750 control chromosomes in the GnomAD database, including 10,232 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 0.35 (10232 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.139-169264C>T		intron_variant		ENST00000506823.6
GALNTL6	XM_017008243.3	c.139-169264C>T		intron_variant
GALNTL6	XM_017008244.3	c.162+7861C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.139-169264C>T		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.87+7861C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52838 AN: 151632 Hom.: 10238 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.407

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.348 AC: 52849 AN: 151750 Hom.: 10232 Cov.: 32 AF XY: 0.352 AC XY: 26076 AN XY: 74160

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.361

Alfa AF: 0.407 Hom.: 6662

Bravo AF: 0.339

Asia WGS AF: 0.499 AC: 1720 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
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: rs6851464; hg19: chr4-172981543;