4-172534095-G-A

Variant names:

• chr4-172534095-G-A
• rs7656178
• NM_001034845.3:c.553+185406G>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.553+185406G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,080 control chromosomes in the GnomAD database, including 3,487 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 0.21 (3487 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.553+185406G>A		intron_variant	Intron 5 of 12	ENST00000506823.6	NP_001030017.2
GALNTL6	XM_017008244.3	c.577+185406G>A		intron_variant	Intron 4 of 11		XP_016863733.1
GALNTL6	XM_011531993.3	c.316+185406G>A		intron_variant	Intron 4 of 11		XP_011530295.1
GALNTL6	XM_017008243.3	c.553+185406G>A		intron_variant	Intron 5 of 9		XP_016863732.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.553+185406G>A		intron_variant	Intron 5 of 12	1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.502+185406G>A		intron_variant	Intron 4 of 11	1		ENSP00000423827.1
GALNTL6	ENST00000457021.1	n.546-11554G>A		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31229 AN: 151962 Hom.: 3478 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00848

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.206 AC: 31265 AN: 152080 Hom.: 3487 Cov.: 32 AF XY: 0.198 AC XY: 14741 AN XY: 74336

African (AFR) AF: 0.279 AC: 11548 AN: 41456

American (AMR) AF: 0.148 AC: 2258 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3466

East Asian (EAS) AF: 0.00850 AC: 44 AN: 5174

South Asian (SAS) AF: 0.0731 AC: 353 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1675 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14257 AN: 67972

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.193 Hom.: 494

Bravo AF: 0.209

Asia WGS AF: 0.0650 AC: 230 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	0.34
DANN	Benign	0.46
PhyloP100		-1.8
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: rs7656178; hg19: chr4-173455246;