9-135637876-G-C

Variant names:

• chr9-135637876-G-C
• rs1537415
• NM_182974.3:c.71+1241C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182974.3(GLT6D1):​c.71+1241C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,996 control chromosomes in the GnomAD database, including 10,213 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 0.36 (10213 hom., cov: 33)
• Consequence: GLT6D1 NM_182974.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 40 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182974.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT6D1	NM_182974.3	MANE Select	c.71+1241C>G		intron	N/A	NP_892019.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GLT6D1	ENST00000371763.6	TSL:1 MANE Select	c.71+1241C>G		intron	N/A	ENSP00000360829.1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55128 AN: 151878 Hom.: 10199 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.363 AC: 55176 AN: 151996 Hom.: 10213 Cov.: 33 AF XY: 0.357 AC XY: 26499 AN XY: 74304

African (AFR) AF: 0.320 AC: 13257 AN: 41448

American (AMR) AF: 0.324 AC: 4948 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1612 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1166 AN: 5182

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4826

European-Finnish (FIN) AF: 0.366 AC: 3870 AN: 10562

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27588 AN: 67944

Other (OTH) AF: 0.377 AC: 796 AN: 2110

Alfa AF: 0.389 Hom.: 6410

Bravo AF: 0.360

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1537415; hg19: chr9-138529722;