7-71665481-A-G

Position:

• chr7-71665481-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_022479.3(GALNT17):​c.1151A>G​(p.Lys384Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GALNT17 NM_022479.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.32

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]

GALNT17 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT17	NM_022479.3	c.1151A>G	p.Lys384Arg	missense_variant	7/11	ENST00000333538.10	NP_071924.1
GALNT17	XM_011516467.4	c.1151A>G	p.Lys384Arg	missense_variant	7/10		XP_011514769.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT17	ENST00000333538.10	c.1151A>G	p.Lys384Arg	missense_variant	7/11	1	NM_022479.3	ENSP00000329654.5
GALNT17	ENST00000467723.1	n.1085A>G		non_coding_transcript_exon_variant	7/11	2
GALNT17	ENST00000498380.6	n.1553A>G		non_coding_transcript_exon_variant	7/11	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 03, 2024

The c.1151A>G (p.K384R) alteration is located in exon 7 (coding exon 7) of the WBSCR17 gene. This alteration results from a A to G substitution at nucleotide position 1151, causing the lysine (K) at amino acid position 384 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.73
BayesDel_addAF	Uncertain	0.046	T
BayesDel_noAF	Benign	-0.17
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.075	T;.
Eigen	Uncertain	0.63
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.79	T;T
M_CAP	Benign	0.044	D
MetaRNN	Uncertain	0.50	T;T
MetaSVM	Benign	-0.63	T
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-2.5	D;.
REVEL	Uncertain	0.32
Sift	Benign	0.043	D;.
Sift4G	Uncertain	0.056	T;T
Polyphen		1.0	D;.
Vest4		0.58
MutPred		0.32		Loss of methylation at K384 (P = 0.0268);.;
MVP		0.82
MPC		1.4
ClinPred		0.95	D
GERP RS		5.8
Varity_R		0.31
gMVP		0.60

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-71130466;