rs73161885

Positions:

• chr7-152113391-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_022087.4(GALNT11):​c.1226A>G​(p.Glu409Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00942 in 1,613,460 control chromosomes in the GnomAD database, including 111 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 0.0093 (11 hom., cov: 32)
  • Exomes 𝑓: 0.0094 (100 hom.)
• Consequence: GALNT11 NM_022087.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.29

Genes affected

GALNT11 (HGNC:19875): (polypeptide N-acetylgalactosaminyltransferase 11) Enables Notch binding activity and polypeptide N-acetylgalactosaminyltransferase activity. Involved in protein O-linked glycosylation via threonine. Predicted to be located in Golgi membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

GALNT11 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.010952532).
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT11	NM_022087.4	c.1226A>G	p.Glu409Gly	missense_variant	8/12	ENST00000430044.7	NP_071370.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT11	ENST00000430044.7	c.1226A>G	p.Glu409Gly	missense_variant	8/12	5	NM_022087.4	ENSP00000395122.2

Frequencies

GnomAD3 genomes AF: 0.00931 AC: 1417 AN: 152190 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00582

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.00430

GnomAD3 exomes AF: 0.00922 AC: 2306 AN: 250150 Hom.: 29 AF XY: 0.00911 AC XY: 1232 AN XY: 135238

Gnomad AFR exome AF: 0.00136

Gnomad AMR exome AF: 0.00323

Gnomad ASJ exome AF: 0.00139

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00181

Gnomad FIN exome AF: 0.0396

Gnomad NFE exome AF: 0.0106

Gnomad OTH exome AF: 0.00858

GnomAD4 exome AF: 0.00943 AC: 13785 AN: 1461152 Hom.: 100 Cov.: 30 AF XY: 0.00934 AC XY: 6789 AN XY: 726846

Gnomad4 AFR exome AF: 0.00117

Gnomad4 AMR exome AF: 0.00287

Gnomad4 ASJ exome AF: 0.00165

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00171

Gnomad4 FIN exome AF: 0.0360

Gnomad4 NFE exome AF: 0.00997

Gnomad4 OTH exome AF: 0.00684

GnomAD4 genome AF: 0.00930 AC: 1416 AN: 152308 Hom.: 11 Cov.: 32 AF XY: 0.0101 AC XY: 753 AN XY: 74466

Gnomad4 AFR AF: 0.00166

Gnomad4 AMR AF: 0.00582

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.00425

Alfa AF: 0.00934 Hom.: 10

Bravo AF: 0.00569

TwinsUK AF: 0.00944 AC: 35

ALSPAC AF: 0.00986 AC: 38

ESP6500AA AF: 0.00204 AC: 9

ESP6500EA AF: 0.00744 AC: 64

ExAC AF: 0.00856 AC: 1039

Asia WGS AF: 0.00260 AC: 10 AN: 3478

EpiCase AF: 0.00740

EpiControl AF: 0.00653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.079	T
BayesDel_noAF	Uncertain	0.13
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.22	T;T
Eigen	Benign	0.16
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.87	.;D
MetaRNN	Benign	0.011	T;T
MetaSVM	Benign	-0.72	T
MutationAssessor	Uncertain	2.1	M;M
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-4.3	D;D
REVEL	Uncertain	0.37
Sift	Benign	0.099	T;T
Sift4G	Benign	0.10	T;T
Polyphen		0.044	B;B
Vest4		0.48
MVP		0.71
MPC		0.31
ClinPred		0.026	T
GERP RS		5.6
Varity_R		0.33
gMVP		0.85

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: rs73161885; hg19: chr7-151810476;