rs11770998

Variant names:

• chr7-71246899-A-G
• rs11770998
• NM_022479.3:c.239-88651A>G

Variant summary

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

The NM_022479.3(GALNT17):​c.239-88651A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 147,232 control chromosomes in the GnomAD database, including 449 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 0.069 (449 hom., cov: 29)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.862
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.239-88651A>G		intron_variant	Intron 1 of 10	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.239-88651A>G		intron_variant	Intron 1 of 9		XP_011514769.1
GALNT17	XM_017012521.3	c.239-88651A>G		intron_variant	Intron 1 of 6		XP_016868010.1
GALNT17	XM_011516469.4	c.239-88651A>G		intron_variant	Intron 1 of 5		XP_011514771.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.239-88651A>G		intron_variant	Intron 1 of 10	1	NM_022479.3	ENSP00000329654.5

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10118 AN: 147180 Hom.: 448 Cov.: 29

Gnomad AFR AF: 0.0161

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.0423

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.0726

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

GnomAD4 genome AF: 0.0687 AC: 10115 AN: 147232 Hom.: 449 Cov.: 29 AF XY: 0.0705 AC XY: 5026 AN XY: 71302

African (AFR) AF: 0.0160 AC: 637 AN: 39760

American (AMR) AF: 0.0645 AC: 933 AN: 14472

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 250 AN: 3430

East Asian (EAS) AF: 0.0423 AC: 207 AN: 4888

South Asian (SAS) AF: 0.0717 AC: 333 AN: 4644

European-Finnish (FIN) AF: 0.153 AC: 1458 AN: 9534

Middle Eastern (MID) AF: 0.0616 AC: 17 AN: 276

European-Non Finnish (NFE) AF: 0.0890 AC: 5990 AN: 67298

Other (OTH) AF: 0.0720 AC: 146 AN: 2028

Alfa AF: 0.0817 Hom.: 286

Bravo AF: 0.0593

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.64
PhyloP100		0.86
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: rs11770998; hg19: chr7-70711885;