chr4-172765357-T-A

Variant names:

• chr4-172765357-T-A
• rs1347706
• NM_001034845.3:c.554-44004T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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.554-44004T>A		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.554-44004T>A		intron	N/A	ENSP00000423313.1	Q49A17-1
	GALNTL6	ENST00000508122.5	TSL:1	c.503-44004T>A		intron	N/A	ENSP00000423827.1	Q49A17-2

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

African (AFR) AF: 0.633 AC: 26251 AN: 41456

American (AMR) AF: 0.494 AC: 7543 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3470

East Asian (EAS) AF: 0.224 AC: 1157 AN: 5172

South Asian (SAS) AF: 0.313 AC: 1509 AN: 4822

European-Finnish (FIN) AF: 0.355 AC: 3750 AN: 10574

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29742 AN: 67922

Other (OTH) AF: 0.471 AC: 992 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.63
PhyloP100		0.0
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: rs1347706; hg19: chr4-173686508;