4-172843426-C-T

Variant names:

• chr4-172843426-C-T
• rs1824347
• NM_001034845.3:c.923+29703C>T

Variant summary

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

The NM_001034845.3(GALNTL6):​c.923+29703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,070 control chromosomes in the GnomAD database, including 19,504 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 0.47 (19504 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.923+29703C>T		intron_variant	Intron 7 of 12	ENST00000506823.6	NP_001030017.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.923+29703C>T		intron_variant	Intron 7 of 12	1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.872+29703C>T		intron_variant	Intron 6 of 11	1		ENSP00000423827.1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70845 AN: 151952 Hom.: 19507 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.466 AC: 70840 AN: 152070 Hom.: 19504 Cov.: 32 AF XY: 0.475 AC XY: 35274 AN XY: 74310

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.488

Alfa AF: 0.531 Hom.: 28713

Bravo AF: 0.450

Asia WGS AF: 0.706 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.15
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: rs1824347; hg19: chr4-173764577;