chr4-172564112-C-T

Position:

• chr4-172564112-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.553+215423C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,964 control chromosomes in the GnomAD database, including 17,472 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 0.45 (17472 hom., cov: 33)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914

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 (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.553+215423C>T		intron_variant		ENST00000506823.6
GALNTL6	XM_011531993.3	c.316+215423C>T		intron_variant
GALNTL6	XM_017008243.3	c.553+215423C>T		intron_variant
GALNTL6	XM_017008244.3	c.577+215423C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.553+215423C>T		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.502+215423C>T		intron_variant		1
GALNTL6	ENST00000457021.1	n.645+18364C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67867 AN: 151846 Hom.: 17466 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.447 AC: 67885 AN: 151964 Hom.: 17472 Cov.: 33 AF XY: 0.455 AC XY: 33827 AN XY: 74280

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.476

Alfa AF: 0.500 Hom.: 4088

Bravo AF: 0.432

Asia WGS AF: 0.571 AC: 1972 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.60

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: rs1472370; hg19: chr4-173485263;