rs7660673

Positions:

• chr4-172875881-C-T

Variant summary

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

The NM_001034845.3(GALNTL6):​c.924-6909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,964 control chromosomes in the GnomAD database, including 5,317 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 0.25 (5317 hom., cov: 32)
• Consequence: GALNTL6 NM_001034845.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNTL6	NM_001034845.3	c.924-6909C>T		intron_variant		ENST00000506823.6	NP_001030017.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNTL6	ENST00000506823.6	c.924-6909C>T		intron_variant		1	NM_001034845.3	ENSP00000423313	P1
GALNTL6	ENST00000508122.5	c.873-6909C>T		intron_variant		1		ENSP00000423827

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38211 AN: 151846 Hom.: 5304 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.252 AC: 38263 AN: 151964 Hom.: 5317 Cov.: 32 AF XY: 0.250 AC XY: 18558 AN XY: 74286

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.0894

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.262

Alfa AF: 0.219 Hom.: 7085

Bravo AF: 0.262

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.25

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: rs7660673; hg19: chr4-173797032;