rs11103117

Positions:

• chr9-135636067-A-G

Variant summary

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

The NM_182974.3(GLT6D1):​c.71+3050T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,164 control chromosomes in the GnomAD database, including 3,859 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 0.21 (3859 hom., cov: 33)
• Consequence: GLT6D1 NM_182974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

GLT6D1 (HGNC:23671): (glycosyltransferase 6 domain containing 1) The GT6 glycosyltransferases gene family, which includes the ABO blood group (ABO; MIM 110300) and GLT6D1, shows a complex evolution pattern, with multiple events of gain and loss in different mammal species. In humans, the ABO gene is considered the sole functional member, although the O allele is null and is fixed in certain populations (summary by Casals et al. (2009) [PubMed 19218399]).[supplied by OMIM, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLT6D1	NM_182974.3	c.71+3050T>C		intron_variant		ENST00000371763.6	NP_892019.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLT6D1	ENST00000371763.6	c.71+3050T>C		intron_variant		1	NM_182974.3	ENSP00000360829.1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31931 AN: 152046 Hom.: 3863 Cov.: 33

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.221

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.210 AC: 31929 AN: 152164 Hom.: 3859 Cov.: 33 AF XY: 0.211 AC XY: 15665 AN XY: 74372

Gnomad4 AFR AF: 0.0880

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.220

Alfa AF: 0.228 Hom.: 1028

Bravo AF: 0.197

Asia WGS AF: 0.257 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.22

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: rs11103117; hg19: chr9-138527913;