4-171895049-A-G

Variant names:

• chr4-171895049-A-G
• rs718913
• NM_001034845.3:c.138+80331A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001034845.3(GALNTL6):​c.138+80331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,060 control chromosomes in the GnomAD database, including 5,514 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 0.27 (5514 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.138+80331A>G		intron_variant	Intron 2 of 12	ENST00000506823.6	NP_001030017.2
GALNTL6	XM_017008243.3	c.138+80331A>G		intron_variant	Intron 2 of 9		XP_016863732.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.138+80331A>G		intron_variant	Intron 2 of 12	1	NM_001034845.3	ENSP00000423313.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40409 AN: 151942 Hom.: 5513 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.266 AC: 40420 AN: 152060 Hom.: 5514 Cov.: 32 AF XY: 0.263 AC XY: 19549 AN XY: 74330

African (AFR) AF: 0.257 AC: 10650 AN: 41458

American (AMR) AF: 0.256 AC: 3908 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1144 AN: 5156

South Asian (SAS) AF: 0.188 AC: 903 AN: 4816

European-Finnish (FIN) AF: 0.273 AC: 2890 AN: 10578

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18953 AN: 67982

Other (OTH) AF: 0.303 AC: 639 AN: 2108

Alfa AF: 0.274 Hom.: 20395

Bravo AF: 0.266

Asia WGS AF: 0.204 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.58
PhyloP100		-1.7
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: rs718913; hg19: chr4-172816200;