rs4129606

Positions:

• chr7-71495908-A-G

Variant summary

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

The NM_022479.3(GALNT17):​c.962+74803A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 152,296 control chromosomes in the GnomAD database, including 247 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 0.041 (247 hom., cov: 32)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

Genes affected

GALNT17 (HGNC:16347): (polypeptide N-acetylgalactosaminyltransferase 17) This gene encodes an N-acetylgalactosaminyltransferase. This gene is located centromeric to the common deleted region in Williams-Beuren syndrome (WBS), a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. This protein may play a role in membrane trafficking. [provided by RefSeq, Jan 2013]

GALNT17 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.962+74803A>G		intron_variant		ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.962+74803A>G		intron_variant			XP_011514769.1
GALNT17	XM_017012521.3	c.962+74803A>G		intron_variant			XP_016868010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.962+74803A>G		intron_variant		1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000467723.1	n.896+74803A>G		intron_variant		2
GALNT17	ENST00000498380.6	n.1364+74803A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0409 AC: 6226 AN: 152178 Hom.: 245 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0204

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00926

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0410 AC: 6240 AN: 152296 Hom.: 247 Cov.: 32 AF XY: 0.0439 AC XY: 3271 AN XY: 74480

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0204

Gnomad4 NFE AF: 0.00926

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0181 Hom.: 61

Bravo AF: 0.0442

Asia WGS AF: 0.112 AC: 389 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	1.8
DANN	Benign	0.63

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: rs4129606; hg19: chr7-70960893;