chr7-141928904-T-C

Variant names:

• chr7-141928904-T-C
• rs11770855
• NM_013252.3:c.*1200A>G

Variant summary

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

The NM_013252.3(CLEC5A):​c.*1200A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,992 control chromosomes in the GnomAD database, including 4,917 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 0.23 (4917 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CLEC5A NM_013252.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 9 publications found

Genes affected

CLEC5A (HGNC:2054): (C-type lectin domain containing 5A) This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type II transmembrane protein interacts with dnax-activation protein 12 and may play a role in cell activation. Alternative splice variants have been described but their full-length sequence has not been determined. [provided by RefSeq, Jul 2008]

MGAM (HGNC:7043): (maltase-glucoamylase) This gene encodes maltase-glucoamylase, which is a brush border membrane enzyme that plays a role in the final steps of digestion of starch. The protein has two catalytic sites identical to those of sucrase-isomaltase, but the proteins are only 59% homologous. Both are members of glycosyl hydrolase family 31, which has a variety of substrate specificities. [provided by RefSeq, Jul 2008]

MGAM Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC5A	NM_013252.3	c.*1200A>G		3_prime_UTR_variant	Exon 7 of 7	ENST00000546910.6	NP_037384.1
CLEC5A	XR_007059995.1	n.1138A>G		non_coding_transcript_exon_variant	Exon 8 of 8
CLEC5A	NM_001301167.2	c.*1200A>G		3_prime_UTR_variant	Exon 6 of 6		NP_001288096.1
CLEC5A	XM_011515995.3	c.*1200A>G		3_prime_UTR_variant	Exon 5 of 5		XP_011514297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC5A	ENST00000546910.6	c.*1200A>G		3_prime_UTR_variant	Exon 7 of 7	1	NM_013252.3	ENSP00000449999.1
MGAM	ENST00000465654.5	c.-179-16917T>C		intron_variant	Intron 1 of 5	3		ENSP00000419372.1
MGAM	ENST00000497554.1	n.37-873T>C		intron_variant	Intron 1 of 2	3
CLEC5A	ENST00000418498.5	n.*1399A>G		downstream_gene_variant		1		ENSP00000392561.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34928 AN: 151876 Hom.: 4919 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.241

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.230 AC: 34924 AN: 151992 Hom.: 4917 Cov.: 32 AF XY: 0.232 AC XY: 17252 AN XY: 74264

African (AFR) AF: 0.0711 AC: 2953 AN: 41504

American (AMR) AF: 0.316 AC: 4824 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 921 AN: 3466

East Asian (EAS) AF: 0.455 AC: 2341 AN: 5146

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2880 AN: 10546

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19146 AN: 67940

Other (OTH) AF: 0.245 AC: 517 AN: 2108

Alfa AF: 0.261 Hom.: 4419

Bravo AF: 0.230

Asia WGS AF: 0.343 AC: 1192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.72
PhyloP100		0.81
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: rs11770855; hg19: chr7-141628704;