rs1901216

chr7-134238095-A-G

Variant summary

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

The NM_144648.3(LRGUK):c.1984-9461A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,236 control chromosomes in the GnomAD database, including 971 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 0.072 (971 hom., cov: 32)
• Consequence: LRGUK NM_144648.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRGUK	NM_144648.3	c.1984-9461A>G		intron_variant		ENST00000285928.3
LRGUK	XM_024446659.2	c.1984-9461A>G		intron_variant
LRGUK	XM_024446661.2	c.1984-9461A>G		intron_variant
LRGUK	XM_047419890.1	c.1777-9461A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRGUK	ENST00000285928.3	c.1984-9461A>G		intron_variant		1	NM_144648.3	P2

Frequencies

GnomAD3 genomes AF: 0.0719 AC: 10944 AN: 152118 Hom.: 968 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0513

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.0110

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00598

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0721 AC: 10970 AN: 152236 Hom.: 971 Cov.: 32 AF XY: 0.0713 AC XY: 5305 AN XY: 74434

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0513

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.0110

Gnomad4 NFE AF: 0.00598

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0346 Hom.: 85

Bravo AF: 0.0813

Asia WGS AF: 0.107 AC: 372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.6
Dann	Benign	0.74

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: rs1901216; hg19: chr7-133922847;