rs17173334

chr7-152094085-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
GALNT11	NM_022087.4	c.-38-105T>G		intron_variant		ENST00000430044.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT11	ENST00000430044.7	c.-38-105T>G		intron_variant		5	NM_022087.4	P1

Frequencies

GnomAD3 genomes AF: 0.0445 AC: 6770 AN: 152184 Hom.: 267 Cov.: 32

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.: 9 AF XY: 0.0422 AC XY: 15764 AN XY: 373292

Gnomad4 AFR exome AF: 0.0625

Gnomad4 AMR exome AF: 0.0764

Gnomad4 ASJ exome AF: 0.0288

Gnomad4 EAS exome AF: 0.205

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.0269

Gnomad4 NFE exome AF: 0.0195

Gnomad4 OTH exome AF: 0.0379

GnomAD4 genome AF: 0.0445 AC: 6774 AN: 152302 Hom.: 266 Cov.: 32 AF XY: 0.0471 AC XY: 3510 AN XY: 74456

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.0544

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0294

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0271 Hom.: 146

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
Dann	Benign	0.54

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

LitVar

Other links and lift over

dbSNP: rs17173334; hg19: chr7-151791170;