Genetic Variant GALNT11:c.-38-105T>G (chr7-152094085-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022087.4(GALNT11):c.-38-105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 875,728 control chromosomes in the GnomAD database, including 1,663 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 0.044 ( 266 hom., cov: 32)

Exomes 𝑓: 0.040 ( 1397 hom. )

Consequence

GALNT11
NM_022087.4 intron

Scores

Splicing: ADA: 0.00005159

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.801

Publications

4 publications found

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:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT11	NM_022087.4 link	c.-38-105T>G		intron_variant	Intron 1 of 11	ENST00000430044.7	NP_071370.2	Q8NCW6-1A0A090N7X6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT11	ENST00000430044.7 link	c.-38-105T>G		intron_variant	Intron 1 of 11	5	NM_022087.4	ENSP00000395122.2		Q8NCW6-1

Frequencies

GnomAD3 genomes

AF:

0.0445

AC:

6770

AN:

152184

Hom.:

267

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0601

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0541

Gnomad ASJ

AF:

0.0282

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0294

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0192

Gnomad OTH

AF:

0.0372

GnomAD4 exome

AF:

0.0400

AC:

28962

AN:

723426

Hom.:

1397

Cov.:

AF XY:

0.0422

AC XY:

15764

AN XY:

373292

show subpopulations

African (AFR)

AF:

0.0625

AC:

1134

AN:

18132

American (AMR)

AF:

0.0764

AC:

1966

AN:

25718

Ashkenazi Jewish (ASJ)

AF:

0.0288

AC:

457

AN:

15882

East Asian (EAS)

AF:

0.205

AC:

7264

AN:

35510

South Asian (SAS)

AF:

0.110

AC:

5924

AN:

53688

European-Finnish (FIN)

AF:

0.0269

AC:

1106

AN:

41058

Middle Eastern (MID)

AF:

0.0374

AC:

137

AN:

3664

European-Non Finnish (NFE)

AF:

0.0195

AC:

9644

AN:

494646

Other (OTH)

AF:

0.0379

AC:

1330

AN:

35128

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1262

2524

3786

5048

6310

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

424

848

1272

1696

2120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0445

AC:

6774

AN:

152302

Hom.:

266

Cov.:

AF XY:

0.0471

AC XY:

3510

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0600

AC:

2496

AN:

41572

American (AMR)

AF:

0.0544

AC:

832

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0282

AC:

AN:

3470

East Asian (EAS)

AF:

0.202

AC:

1047

AN:

5172

South Asian (SAS)

AF:

0.123

AC:

595

AN:

4826

European-Finnish (FIN)

AF:

0.0294

AC:

312

AN:

10612

Middle Eastern (MID)

AF:

0.0136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0192

AC:

1307

AN:

68030

Other (OTH)

AF:

0.0364

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

323

646

970

1293

1616

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0284

Hom.:

188

Bravo

AF:

0.0473

Asia WGS

AF:

0.160

AC:

556

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

9.1

(source)

DANN

Benign

0.54

PhyloP100

0.80

PromoterAI

-0.0079

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000052

dbscSNV1_RF

Benign

0.0060

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over