7-71417177-T-C

Position:

• chr7-71417177-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.764+1114T>C		intron_variant		ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.764+1114T>C		intron_variant			XP_011514769.1
GALNT17	XM_011516469.4	c.764+1114T>C		intron_variant			XP_011514771.1
GALNT17	XM_017012521.3	c.764+1114T>C		intron_variant			XP_016868010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.764+1114T>C		intron_variant		1	NM_022479.3	ENSP00000329654	P1
GALNT17	ENST00000467723.1	n.698+1114T>C		intron_variant, non_coding_transcript_variant		2
GALNT17	ENST00000498380.6	n.1166+1114T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0930

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0647

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0644 Hom.: 463

Bravo AF: 0.0709

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs7798395; hg19: chr7-70882163;