chr4-172060392-C-T

Variant names:

• chr4-172060392-C-T
• rs6851464
• NM_001034845.3:c.139-169264C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001034845.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNTL6	NM_001034845.3	MANE Select	c.139-169264C>T		intron	N/A	NP_001030017.2	Q49A17-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNTL6	ENST00000506823.6	TSL:1 MANE Select	c.139-169264C>T		intron	N/A	ENSP00000423313.1	Q49A17-1
	GALNTL6	ENST00000508122.5	TSL:1	c.87+7861C>T		intron	N/A	ENSP00000423827.1	Q49A17-2

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

African (AFR) AF: 0.172 AC: 7119 AN: 41386

American (AMR) AF: 0.366 AC: 5573 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2412 AN: 5144

South Asian (SAS) AF: 0.524 AC: 2527 AN: 4818

European-Finnish (FIN) AF: 0.363 AC: 3807 AN: 10494

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28816 AN: 67890

Other (OTH) AF: 0.361 AC: 762 AN: 2112

Alfa AF: 0.403 Hom.: 7556

Bravo AF: 0.339

Asia WGS AF: 0.499 AC: 1720 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.44
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6851464; hg19: chr4-172981543;