rs4521648

Variant names:

• chr7-71464650-C-T
• rs4521648
• NM_022479.3:c.962+43545C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022479.3(GALNT17):​c.962+43545C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,046 control chromosomes in the GnomAD database, including 1,734 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 0.11 (1734 hom., cov: 32)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.962+43545C>T		intron_variant	Intron 5 of 10	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.962+43545C>T		intron_variant	Intron 5 of 9		XP_011514769.1
GALNT17	XM_017012521.3	c.962+43545C>T		intron_variant	Intron 5 of 6		XP_016868010.1
GALNT17	XM_011516469.4	c.963-21782C>T		intron_variant	Intron 5 of 5		XP_011514771.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.962+43545C>T		intron_variant	Intron 5 of 10	1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000467723.1	n.896+43545C>T		intron_variant	Intron 5 of 10	2
GALNT17	ENST00000498380.6	n.1364+43545C>T		intron_variant	Intron 5 of 10	2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16691 AN: 151928 Hom.: 1735 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.110 AC: 16691 AN: 152046 Hom.: 1734 Cov.: 32 AF XY: 0.118 AC XY: 8750 AN XY: 74330

African (AFR) AF: 0.0249 AC: 1032 AN: 41496

American (AMR) AF: 0.154 AC: 2355 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3472

East Asian (EAS) AF: 0.545 AC: 2800 AN: 5142

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4818

European-Finnish (FIN) AF: 0.111 AC: 1177 AN: 10558

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7134 AN: 67980

Other (OTH) AF: 0.134 AC: 282 AN: 2110

Alfa AF: 0.111 Hom.: 1889

Bravo AF: 0.112

Asia WGS AF: 0.346 AC: 1199 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	4.0
DANN	Benign	0.78
PhyloP100		0.17
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: rs4521648; hg19: chr7-70929635;