chr4-172545070-T-A

Variant names:

• chr4-172545070-T-A
• rs337997
• NM_001034845.3:c.553+196381T>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+196381T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,274 control chromosomes in the GnomAD database, including 996 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 0.11 (996 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• 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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.553+196381T>A		intron_variant	Intron 5 of 12	ENST00000506823.6	NP_001030017.2
GALNTL6	XM_017008244.3	c.577+196381T>A		intron_variant	Intron 4 of 11		XP_016863733.1
GALNTL6	XM_011531993.3	c.316+196381T>A		intron_variant	Intron 4 of 11		XP_011530295.1
GALNTL6	XM_017008243.3	c.553+196381T>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+196381T>A		intron_variant	Intron 5 of 12	1	NM_001034845.3	ENSP00000423313.1
GALNTL6	ENST00000508122.5	c.502+196381T>A		intron_variant	Intron 4 of 11	1		ENSP00000423827.1
GALNTL6	ENST00000457021.1	n.546-579T>A		intron_variant	Intron 4 of 5	1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16333 AN: 152156 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.107 AC: 16339 AN: 152274 Hom.: 996 Cov.: 32 AF XY: 0.108 AC XY: 8035 AN XY: 74452

African (AFR) AF: 0.0454 AC: 1887 AN: 41570

American (AMR) AF: 0.137 AC: 2091 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1174 AN: 5188

South Asian (SAS) AF: 0.115 AC: 556 AN: 4826

European-Finnish (FIN) AF: 0.0999 AC: 1060 AN: 10612

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8773 AN: 68008

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.108 Hom.: 108

Bravo AF: 0.110

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.66
DANN	Benign	0.72
PhyloP100		-0.43
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: rs337997; hg19: chr4-173466221;