NM_022479.3:c.1500+12392A>G

Variant names:

• chr7-71689698-A-G
• rs2079961
• NM_022479.3:c.1500+12392A>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.1500+12392A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,126 control chromosomes in the GnomAD database, including 43,436 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 0.75 (43436 hom., cov: 33)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445
• 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 (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.1500+12392A>G		intron_variant	Intron 9 of 10	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.1500+12392A>G		intron_variant	Intron 9 of 9		XP_011514769.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.1500+12392A>G		intron_variant	Intron 9 of 10	1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000467723.1	n.1434+12392A>G		intron_variant	Intron 9 of 10	2
GALNT17	ENST00000498380.6	n.1902+12392A>G		intron_variant	Intron 9 of 10	2

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114682 AN: 152008 Hom.: 43406 Cov.: 33

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.754 AC: 114765 AN: 152126 Hom.: 43436 Cov.: 33 AF XY: 0.755 AC XY: 56168 AN XY: 74362

African (AFR) AF: 0.787 AC: 32688 AN: 41514

American (AMR) AF: 0.797 AC: 12175 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2665 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4392 AN: 5154

South Asian (SAS) AF: 0.837 AC: 4039 AN: 4824

European-Finnish (FIN) AF: 0.679 AC: 7175 AN: 10562

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48978 AN: 68002

Other (OTH) AF: 0.776 AC: 1639 AN: 2112

Alfa AF: 0.734 Hom.: 6947

Bravo AF: 0.767

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.45
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: rs2079961; hg19: chr7-71154683;