rs11537930

Variant names:

• chr11-66347429-C-T
• rs11537930
• NM_006876.3:c.117G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-66347429-C-T
• chr11-66347429-C-G

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_006876.3(B4GAT1):​c.117G>A​(p.Gln39Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 1,573,756 control chromosomes in the GnomAD database, including 7,658 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1486 hom., cov: 32)
  • Exomes 𝑓: 0.088 (6172 hom.)
• Consequence: B4GAT1 NM_006876.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 1.16
• Publications: 26 publications found

Genes affected

B4GAT1 (HGNC:15685): (beta-1,4-glucuronyltransferase 1) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein. It is essential for the synthesis of poly-N-acetyllactosamine, a determinant for the blood group i antigen. [provided by RefSeq, Jul 2008]

B4GAT1 Gene-Disease associations (from GenCC):

• muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)
• muscular dystrophy-dystroglycanopathy, type A

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BP6: Variant 11-66347429-C-T is Benign according to our data. Variant chr11-66347429-C-T is described in ClinVar as Benign. ClinVar VariationId is 260057.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.16 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006876.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B4GAT1	NM_006876.3	MANE Select	c.117G>A	p.Gln39Gln	synonymous	Exon 1 of 2	NP_006867.1	O43505

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B4GAT1	ENST00000311181.5	TSL:1 MANE Select	c.117G>A	p.Gln39Gln	synonymous	Exon 1 of 2	ENSP00000309096.4	O43505
	B4GAT1	ENST00000865226.1		c.117G>A	p.Gln39Gln	synonymous	Exon 1 of 2	ENSP00000535285.1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18650 AN: 152138 Hom.: 1486 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0492

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.115

GnomAD2 exomes AF: 0.0956 AC: 19153 AN: 200426 AF XY: 0.0928

Gnomad AFR exome AF: 0.237

Gnomad AMR exome AF: 0.0543

Gnomad ASJ exome AF: 0.111

Gnomad EAS exome AF: 0.186

Gnomad FIN exome AF: 0.0536

Gnomad NFE exome AF: 0.0892

Gnomad OTH exome AF: 0.0873

GnomAD4 exome AF: 0.0875 AC: 124447 AN: 1421500 Hom.: 6172 Cov.: 32 AF XY: 0.0862 AC XY: 60645 AN XY: 703164

African (AFR) AF: 0.234 AC: 7617 AN: 32524

American (AMR) AF: 0.0583 AC: 2315 AN: 39686

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 2436 AN: 23940

East Asian (EAS) AF: 0.167 AC: 6477 AN: 38704

South Asian (SAS) AF: 0.0543 AC: 4333 AN: 79834

European-Finnish (FIN) AF: 0.0553 AC: 2790 AN: 50460

Middle Eastern (MID) AF: 0.115 AC: 647 AN: 5624

European-Non Finnish (NFE) AF: 0.0844 AC: 92218 AN: 1092128

Other (OTH) AF: 0.0958 AC: 5614 AN: 58600

GnomAD4 genome AF: 0.123 AC: 18673 AN: 152256 Hom.: 1486 Cov.: 32 AF XY: 0.119 AC XY: 8849 AN XY: 74454

African (AFR) AF: 0.227 AC: 9424 AN: 41544

American (AMR) AF: 0.0861 AC: 1317 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3472

East Asian (EAS) AF: 0.169 AC: 873 AN: 5170

South Asian (SAS) AF: 0.0501 AC: 242 AN: 4832

European-Finnish (FIN) AF: 0.0474 AC: 503 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5639 AN: 68010

Other (OTH) AF: 0.113 AC: 239 AN: 2108

Alfa AF: 0.103 Hom.: 1186

Bravo AF: 0.132

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not specified (2)
-	-	1	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.6
DANN	Benign	0.94
PhyloP100		1.2
PromoterAI		-0.031	Neutral
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: rs11537930; hg19: chr11-66114900; COSMIC: COSV60820002; COSMIC: COSV60820002;