chr4-173173789-G-A

Position:

• chr4-173173789-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_017423.3(GALNT7):​c.126+4828G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,196 control chromosomes in the GnomAD database, including 91 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 0.031 (91 hom., cov: 32)
• Consequence: GALNT7 NM_017423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

Genes affected

GALNT7 (HGNC:4129): (polypeptide N-acetylgalactosaminyltransferase 7) This gene encodes GalNAc transferase 7, a member of the GalNAc-transferase family. The enzyme encoded by this gene controls the initiation step of mucin-type O-linked protein glycosylation and transfer of N-acetylgalactosamine to serine and threonine amino acid residues. This enzyme is a type II transmembrane protein and shares common sequence motifs with other family members. Unlike other family members, this enzyme shows exclusive specificity for partially GalNAc-glycosylated acceptor substrates and shows no activity with non-glycosylated peptides. This protein may function as a follow-up enzyme in the initiation step of O-glycosylation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0305 (4644/152196) while in subpopulation NFE AF= 0.0481 (3271/68020). AF 95% confidence interval is 0.0467. There are 91 homozygotes in gnomad4. There are 2155 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 91 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT7	NM_017423.3	c.126+4828G>A		intron_variant		ENST00000265000.9	NP_059119.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT7	ENST00000265000.9	c.126+4828G>A		intron_variant		1	NM_017423.3	ENSP00000265000	P3
GALNT7	ENST00000505308.6	c.126+4828G>A		intron_variant		2		ENSP00000427095	A1
GALNT7	ENST00000512285.5	c.126+4828G>A		intron_variant		5		ENSP00000427050

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 4646 AN: 152078 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.00884

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.0302

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0336

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

GnomAD4 genome AF: 0.0305 AC: 4644 AN: 152196 Hom.: 91 Cov.: 32 AF XY: 0.0290 AC XY: 2155 AN XY: 74400

Gnomad4 AFR AF: 0.00881

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.0302

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0413 Hom.: 25

Bravo AF: 0.0292

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.48
DANN	Benign	0.26

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: rs62341097; hg19: chr4-174094940;