NM_022479.3:c.423-23643G>T

Variant names:

• chr7-71364592-G-T
• rs17143419
• NM_022479.3:c.423-23643G>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.423-23643G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0956 in 152,176 control chromosomes in the GnomAD database, including 707 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 0.096 (707 hom., cov: 32)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.423-23643G>T		intron_variant	Intron 2 of 10	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.423-23643G>T		intron_variant	Intron 2 of 9		XP_011514769.1
GALNT17	XM_017012521.3	c.423-23643G>T		intron_variant	Intron 2 of 6		XP_016868010.1
GALNT17	XM_011516469.4	c.423-23643G>T		intron_variant	Intron 2 of 5		XP_011514771.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.423-23643G>T		intron_variant	Intron 2 of 10	1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000447516.5	c.357-23643G>T		intron_variant	Intron 2 of 3	4		ENSP00000392019.1
GALNT17	ENST00000467723.1	n.357-23643G>T		intron_variant	Intron 2 of 10	2
GALNT17	ENST00000498380.6	n.825-23643G>T		intron_variant	Intron 2 of 10	2

Frequencies

GnomAD3 genomes AF: 0.0955 AC: 14527 AN: 152058 Hom.: 704 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0956 AC: 14548 AN: 152176 Hom.: 707 Cov.: 32 AF XY: 0.0934 AC XY: 6953 AN XY: 74418

African (AFR) AF: 0.128 AC: 5298 AN: 41500

American (AMR) AF: 0.0938 AC: 1434 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 224 AN: 3472

East Asian (EAS) AF: 0.0672 AC: 348 AN: 5180

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4822

European-Finnish (FIN) AF: 0.0844 AC: 894 AN: 10596

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0872 AC: 5931 AN: 68008

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.0899 Hom.: 917

Bravo AF: 0.0973

Asia WGS AF: 0.0600 AC: 206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
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: rs17143419; hg19: chr7-70829578;