rs4719147

chr7-71551174-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022479.3(GALNT17):c.963-20111T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,924 control chromosomes in the GnomAD database, including 32,037 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 0.64 (32037 hom., cov: 32)
• Consequence: GALNT17 NM_022479.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT17	NM_022479.3	c.963-20111T>G		intron_variant		ENST00000333538.10
GALNT17	XM_011516467.4	c.963-20111T>G		intron_variant
GALNT17	XM_017012521.3	c.963-20111T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT17	ENST00000333538.10	c.963-20111T>G		intron_variant		1	NM_022479.3	P1
GALNT17	ENST00000467723.1	n.897-20111T>G		intron_variant, non_coding_transcript_variant		2
GALNT17	ENST00000498380.6	n.1365-20111T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97066 AN: 151806 Hom.: 32037 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.751

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.639 AC: 97101 AN: 151924 Hom.: 32037 Cov.: 32 AF XY: 0.636 AC XY: 47246 AN XY: 74250

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.751

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.653

Alfa AF: 0.699 Hom.: 41719

Bravo AF: 0.634

Asia WGS AF: 0.481 AC: 1676 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.84

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: rs4719147; hg19: chr7-71016159; COSMIC: COSV61194155;