chr7-134167429-C-G

Position:

• chr7-134167429-C-G

Variant summary

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

The NM_144648.3(LRGUK):​c.939+3889C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,230 control chromosomes in the GnomAD database, including 1,679 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 0.13 (1679 hom., cov: 32)
• Consequence: LRGUK NM_144648.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

Genes affected

LRGUK (HGNC:21964): (leucine rich repeats and guanylate kinase domain containing) Predicted to enable guanylate kinase activity. Predicted to be involved in axoneme assembly and spermatogenesis. Predicted to be located in acrosomal vesicle and manchette. Predicted to be active in cytosol. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRGUK	NM_144648.3	c.939+3889C>G		intron_variant		ENST00000285928.3	NP_653249.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRGUK	ENST00000285928.3	c.939+3889C>G		intron_variant		1	NM_144648.3	ENSP00000285928	P2
LRGUK	ENST00000645682.1	c.939+3889C>G		intron_variant				ENSP00000495637	A2
LRGUK	ENST00000695542.2	c.939+3889C>G		intron_variant				ENSP00000511999	A2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20024 AN: 152112 Hom.: 1669 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0596

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.132 AC: 20069 AN: 152230 Hom.: 1679 Cov.: 32 AF XY: 0.132 AC XY: 9855 AN XY: 74438

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0596

Gnomad4 NFE AF: 0.0931

Gnomad4 OTH AF: 0.143

Alfa AF: 0.112 Hom.: 144

Bravo AF: 0.144

Asia WGS AF: 0.235 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.76

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: rs892984; hg19: chr7-133852181;