dbSNP rs62341097: GALNT7:c.126+4828G>A (chr4-173173789-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.708

Publications

7 publications found

Variant links:

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]

GALNT7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 91 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT7	NM_017423.3 link	c.126+4828G>A		intron_variant	Intron 1 of 11	ENST00000265000.9	NP_059119.2	Q86SF2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GALNT7	ENST00000265000.9 link	c.126+4828G>A	intron_variant	Intron 1 of 11	1	NM_017423.3	ENSP00000265000.4	Q86SF2
GALNT7	ENST00000505308.6 link	c.126+4828G>A	intron_variant	Intron 1 of 11	2		ENSP00000427095.2	H0YAH3
GALNT7	ENST00000512285.5 link	c.126+4828G>A	intron_variant	Intron 1 of 5	5		ENSP00000427050.1	E9PBY3

Frequencies

GnomAD3 genomes

AF:

0.0306

AC:

4646

AN:

152078

Hom.:

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.0290

AC XY:

2155

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.00881

AC:

366

AN:

41536

American (AMR)

AF:

0.0218

AC:

333

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0245

AC:

AN:

3470

East Asian (EAS)

AF:

0.0141

AC:

AN:

5180

South Asian (SAS)

AF:

0.0247

AC:

119

AN:

4812

European-Finnish (FIN)

AF:

0.0302

AC:

320

AN:

10582

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0481

AC:

3271

AN:

68020

Other (OTH)

AF:

0.0346

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

243

486

730

973

1216

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

168

224

280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0433

Hom.:

276

Bravo

AF:

0.0292

Asia WGS

AF:

0.0240

AC:

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

(source)

DANN

Benign

0.26

PhyloP100

-0.71

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over