7-71535629-T-G

Variant names:

• chr7-71535629-T-G
• rs6460664
• NM_022479.3:c.963-35656T>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.963-35656T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,998 control chromosomes in the GnomAD database, including 14,617 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 0.42 (14617 hom., cov: 33)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.963-35656T>G		intron_variant	Intron 5 of 10	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.963-35656T>G		intron_variant	Intron 5 of 9		XP_011514769.1
GALNT17	XM_017012521.3	c.963-35656T>G		intron_variant	Intron 5 of 6		XP_016868010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.963-35656T>G		intron_variant	Intron 5 of 10	1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000467723.1	n.897-35656T>G		intron_variant	Intron 5 of 10	2
GALNT17	ENST00000498380.6	n.1365-35656T>G		intron_variant	Intron 5 of 10	2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64272 AN: 151880 Hom.: 14609 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.423 AC: 64309 AN: 151998 Hom.: 14617 Cov.: 33 AF XY: 0.417 AC XY: 30948 AN XY: 74282

African (AFR) AF: 0.598 AC: 24787 AN: 41464

American (AMR) AF: 0.401 AC: 6121 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5174

South Asian (SAS) AF: 0.260 AC: 1252 AN: 4818

European-Finnish (FIN) AF: 0.310 AC: 3274 AN: 10548

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25135 AN: 67944

Other (OTH) AF: 0.404 AC: 855 AN: 2114

Alfa AF: 0.384 Hom.: 35417

Bravo AF: 0.438

Asia WGS AF: 0.267 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.64
PhyloP100		0.079
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: rs6460664; hg19: chr7-71000614;