7-134233831-C-T

Position:

• chr7-134233831-C-T

Variant summary

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

The NM_144648.3(LRGUK):​c.1983+11913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0518 in 152,224 control chromosomes in the GnomAD database, including 455 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 0.052 (455 hom., cov: 32)
• Consequence: LRGUK NM_144648.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRGUK	NM_144648.3	c.1983+11913C>T		intron_variant		ENST00000285928.3	NP_653249.1
LRGUK	XM_024446659.2	c.1983+11913C>T		intron_variant			XP_024302427.1
LRGUK	XM_024446661.2	c.1983+11913C>T		intron_variant			XP_024302429.1
LRGUK	XM_047419890.1	c.1776+11913C>T		intron_variant			XP_047275846.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRGUK	ENST00000285928.3	c.1983+11913C>T		intron_variant		1	NM_144648.3	ENSP00000285928	P2

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7858 AN: 152106 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00572

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0518 AC: 7887 AN: 152224 Hom.: 455 Cov.: 32 AF XY: 0.0515 AC XY: 3835 AN XY: 74416

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0463

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.0610

Gnomad4 FIN AF: 0.0112

Gnomad4 NFE AF: 0.00572

Gnomad4 OTH AF: 0.0446

Alfa AF: 0.00931 Hom.: 7

Bravo AF: 0.0593

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.90

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: rs1558996; hg19: chr7-133918583;