rs11772787

Variant names:

• chr7-71254236-A-G
• rs11772787
• NM_022479.3:c.239-81314A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-71254236-A-G
• chr7-71254236-A-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.239-81314A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,062 control chromosomes in the GnomAD database, including 6,234 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 0.28 (6234 hom., cov: 32)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 3 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.239-81314A>G		intron_variant	Intron 1 of 10	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.239-81314A>G		intron_variant	Intron 1 of 9		XP_011514769.1
GALNT17	XM_017012521.3	c.239-81314A>G		intron_variant	Intron 1 of 6		XP_016868010.1
GALNT17	XM_011516469.4	c.239-81314A>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.239-81314A>G		intron_variant	Intron 1 of 10	1	NM_022479.3	ENSP00000329654.5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42322 AN: 151944 Hom.: 6216 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.279 AC: 42374 AN: 152062 Hom.: 6234 Cov.: 32 AF XY: 0.282 AC XY: 20934 AN XY: 74322

African (AFR) AF: 0.341 AC: 14146 AN: 41498

American (AMR) AF: 0.172 AC: 2632 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 647 AN: 3466

East Asian (EAS) AF: 0.338 AC: 1735 AN: 5140

South Asian (SAS) AF: 0.380 AC: 1828 AN: 4816

European-Finnish (FIN) AF: 0.312 AC: 3299 AN: 10558

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17286 AN: 67980

Other (OTH) AF: 0.263 AC: 555 AN: 2114

Alfa AF: 0.256 Hom.: 16704

Bravo AF: 0.268

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.33
PhyloP100		-0.50
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: rs11772787; hg19: chr7-70719222;