rs7676941

chr4-172839412-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001034845.3(GALNTL6):c.923+25689A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,060 control chromosomes in the GnomAD database, including 11,293 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 0.31 (11293 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNTL6	NM_001034845.3	c.923+25689A>C		intron_variant		ENST00000506823.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNTL6	ENST00000506823.6	c.923+25689A>C		intron_variant		1	NM_001034845.3	P1
GALNTL6	ENST00000508122.5	c.872+25689A>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47179 AN: 151942 Hom.: 11269 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.311 AC: 47252 AN: 152060 Hom.: 11293 Cov.: 32 AF XY: 0.312 AC XY: 23214 AN XY: 74338

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.252

Alfa AF: 0.244 Hom.: 1175

Bravo AF: 0.333

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.11
Dann	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs7676941; hg19: chr4-173760563;