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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022087.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GALNT11	NM_022087.4	MANE Select	c.-38-105T>G	intron	N/A	NP_071370.2
GALNT11	NM_001371464.1		c.-38-105T>G	intron	N/A	NP_001358393.1
GALNT11	NM_001371458.1		c.-38-105T>G	intron	N/A	NP_001358387.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
GALNT11	ENST00000430044.7	TSL:5 MANE Select	c.-38-105T>G	intron	N/A	ENSP00000395122.2
GALNT11	ENST00000415421.5	TSL:1	c.-38-105T>G	intron	N/A	ENSP00000410093.1
GALNT11	ENST00000447796.1	TSL:3	c.-143T>G	5_prime_UTR	Exon 1 of 3	ENSP00000412142.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over