NM_022479.3:c.963-15963T>C

Variant names:

• chr7-71555322-T-C
• rs6460671
• NM_022479.3:c.963-15963T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022479.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT17	NM_022479.3	MANE Select	c.963-15963T>C		intron	N/A	NP_071924.1	Q6IS24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT17	ENST00000333538.10	TSL:1 MANE Select	c.963-15963T>C		intron	N/A	ENSP00000329654.5	Q6IS24
	GALNT17	ENST00000467723.1	TSL:2	n.897-15963T>C		intron	N/A
	GALNT17	ENST00000498380.6	TSL:2	n.1365-15963T>C		intron	N/A

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

African (AFR) AF: 0.322 AC: 13336 AN: 41384

American (AMR) AF: 0.343 AC: 5231 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3466

East Asian (EAS) AF: 0.223 AC: 1146 AN: 5142

South Asian (SAS) AF: 0.233 AC: 1119 AN: 4802

European-Finnish (FIN) AF: 0.283 AC: 2980 AN: 10524

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.331 AC: 22492 AN: 67898

Other (OTH) AF: 0.329 AC: 690 AN: 2100

Alfa AF: 0.328 Hom.: 36421

Bravo AF: 0.328

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.39
PhyloP100		1.3
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: rs6460671; hg19: chr7-71020307;