Variant chr7-152103143-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_022087.4(GALNT11):c.451C>T(p.Pro151Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00496 in 1,610,020 control chromosomes in the GnomAD database, including 330 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.027 ( 181 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 149 hom. )

Consequence

GALNT11
NM_022087.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 7.84

Variant links:

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 links:

GALNT11 (HGNC:):

GALNT11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0031830072).

BP6

Variant 7-152103143-C-T is Benign according to our data. Variant chr7-152103143-C-T is described in ClinVar as [Benign]. Clinvar id is 780727.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT11	NM_022087.4 linkuse as main transcript	c.451C>T	p.Pro151Ser	missense_variant	4/12	ENST00000430044.7	NP_071370.2	Q8NCW6-1A0A090N7X6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT11	ENST00000430044.7 linkuse as main transcript	c.451C>T	p.Pro151Ser	missense_variant	4/12	5	NM_022087.4	ENSP00000395122.2		Q8NCW6-1

Frequencies

GnomAD3 genomes

AF:

0.0268

AC:

4076

AN:

152154

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0925

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.000353

Gnomad OTH

AF:

0.0215

GnomAD3 exomes

AF:

0.00692

AC:

1739

AN:

251420

Hom.:

AF XY:

0.00489

AC XY:

665

AN XY:

135882

show subpopulations

Gnomad AFR exome

AF:

0.0933

Gnomad AMR exome

AF:

0.00483

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000653

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000255

Gnomad OTH exome

AF:

0.00391

GnomAD4 exome

AF:

0.00267

AC:

3891

AN:

1457748

Hom.:

149

Cov.:

AF XY:

0.00233

AC XY:

1685

AN XY:

724514

show subpopulations

Gnomad4 AFR exome

AF:

0.0943

Gnomad4 AMR exome

AF:

0.00564

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000105

Gnomad4 OTH exome

AF:

0.00539

GnomAD4 genome

AF:

0.0269

AC:

4094

AN:

152272

Hom.:

181

Cov.:

AF XY:

0.0263

AC XY:

1957

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0928

Gnomad4 AMR

AF:

0.0106

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000353

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.00417

Hom.:

Bravo

AF:

0.0295

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.0974

AC:

429

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.00870

AC:

1056

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.000327

EpiControl

AF:

0.000415

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.29

BayesDel_noAF

Benign

-0.11

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.32

T;T;T;.;.;T;T

Eigen

Pathogenic

0.84

Eigen_PC

Pathogenic

0.73

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.95

.;D;D;.;D;D;D

MetaRNN

Benign

0.0032

T;T;T;T;T;T;T

MetaSVM

Benign

-0.56

MutationAssessor

Pathogenic

3.6

H;.;H;H;H;.;.

PrimateAI

Uncertain

0.55

PROVEAN

Pathogenic

-7.2

D;D;D;D;.;D;D

REVEL

Uncertain

0.35

Sift

Benign

0.038

D;D;D;D;.;D;D

Sift4G

Uncertain

0.047

D;D;D;T;T;D;D

Polyphen

1.0

D;.;D;D;D;.;.

Vest4

0.86

MVP

0.91

MPC

0.93

ClinPred

0.073

GERP RS

5.0

Varity_R

0.72

gMVP

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over