7-71417177-T-C

Variant names:

• chr7-71417177-T-C
• rs7798395
• NM_022479.3:c.764+1114T>C

Variant summary

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

The NM_022479.3(GALNT17):​c.764+1114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 152,250 control chromosomes in the GnomAD database, including 462 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 0.074 (462 hom., cov: 32)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022479.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT17	NM_022479.3	MANE Select	c.764+1114T>C		intron	N/A	NP_071924.1	Q6IS24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT17	ENST00000333538.10	TSL:1 MANE Select	c.764+1114T>C		intron	N/A	ENSP00000329654.5	Q6IS24
	GALNT17	ENST00000467723.1	TSL:2	n.698+1114T>C		intron	N/A
	GALNT17	ENST00000498380.6	TSL:2	n.1166+1114T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0739 AC: 11250 AN: 152132 Hom.: 463 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0549

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.0659

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

GnomAD4 genome AF: 0.0740 AC: 11266 AN: 152250 Hom.: 462 Cov.: 32 AF XY: 0.0746 AC XY: 5551 AN XY: 74434

African (AFR) AF: 0.0930 AC: 3864 AN: 41548

American (AMR) AF: 0.0547 AC: 837 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.0671 AC: 348 AN: 5186

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4824

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0647 AC: 4403 AN: 68012

Other (OTH) AF: 0.0657 AC: 139 AN: 2116

Alfa AF: 0.0652 Hom.: 595

Bravo AF: 0.0709

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.73
PhyloP100		-1.4
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: rs7798395; hg19: chr7-70882163;