7-71555322-T-C

Position:

• chr7-71555322-T-C

Variant summary

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

The NM_022479.3(GALNT17):​c.963-15963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 151,750 control chromosomes in the GnomAD database, including 7,948 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 0.32 (7948 hom., cov: 31)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.963-15963T>C		intron_variant		ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.963-15963T>C		intron_variant			XP_011514769.1
GALNT17	XM_017012521.3	c.963-15963T>C		intron_variant			XP_016868010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.963-15963T>C		intron_variant		1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000467723.1	n.897-15963T>C		intron_variant		2
GALNT17	ENST00000498380.6	n.1365-15963T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48660 AN: 151634 Hom.: 7948 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.321 AC: 48684 AN: 151750 Hom.: 7948 Cov.: 31 AF XY: 0.318 AC XY: 23591 AN XY: 74164

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.329

Alfa AF: 0.330 Hom.: 17130

Bravo AF: 0.328

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.39

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: rs6460671; hg19: chr7-71020307;