4-173030462-A-G

Variant names:

• chr4-173030462-A-G
• rs3905287
• NM_001034845.3:c.1638+8837A>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.1638+8837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,938 control chromosomes in the GnomAD database, including 9,897 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 (9897 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 6 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.1638+8837A>G		intron_variant	Intron 12 of 12	ENST00000506823.6	NP_001030017.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.1638+8837A>G		intron_variant	Intron 12 of 12	1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.1587+8837A>G		intron_variant	Intron 11 of 11	1		ENSP00000423827.1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53398 AN: 151820 Hom.: 9869 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0909

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.352 AC: 53469 AN: 151938 Hom.: 9897 Cov.: 32 AF XY: 0.344 AC XY: 25550 AN XY: 74252

African (AFR) AF: 0.436 AC: 18053 AN: 41406

American (AMR) AF: 0.354 AC: 5407 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3470

East Asian (EAS) AF: 0.0905 AC: 468 AN: 5170

South Asian (SAS) AF: 0.198 AC: 954 AN: 4816

European-Finnish (FIN) AF: 0.307 AC: 3237 AN: 10538

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23225 AN: 67942

Other (OTH) AF: 0.328 AC: 692 AN: 2112

Alfa AF: 0.337 Hom.: 7740

Bravo AF: 0.363

Asia WGS AF: 0.179 AC: 623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.98
DANN	Benign	0.28
PhyloP100		-0.31
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: rs3905287; hg19: chr4-173951613;