rs2544165

Variant names:

• chr7-134235691-G-A
• rs2544165
• NM_144648.3:c.1984-11865G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-134235691-G-A
• chr7-134235691-G-C

Variant summary

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

The NM_144648.3(LRGUK):​c.1984-11865G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,942 control chromosomes in the GnomAD database, including 16,739 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 0.47 (16739 hom., cov: 32)
• Consequence: LRGUK NM_144648.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 11 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRGUK	NM_144648.3	c.1984-11865G>A		intron_variant	Intron 16 of 19	ENST00000285928.3	NP_653249.1
LRGUK	XM_024446659.2	c.1984-11865G>A		intron_variant	Intron 16 of 19		XP_024302427.1
LRGUK	XM_024446661.2	c.1984-11865G>A		intron_variant	Intron 16 of 19		XP_024302429.1
LRGUK	XM_047419890.1	c.1777-11865G>A		intron_variant	Intron 14 of 17		XP_047275846.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRGUK	ENST00000285928.3	c.1984-11865G>A		intron_variant	Intron 16 of 19	1	NM_144648.3	ENSP00000285928.2

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70674 AN: 151824 Hom.: 16687 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.466 AC: 70783 AN: 151942 Hom.: 16739 Cov.: 32 AF XY: 0.466 AC XY: 34576 AN XY: 74264

African (AFR) AF: 0.491 AC: 20325 AN: 41434

American (AMR) AF: 0.542 AC: 8266 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1134 AN: 5168

South Asian (SAS) AF: 0.568 AC: 2732 AN: 4814

European-Finnish (FIN) AF: 0.390 AC: 4109 AN: 10538

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31457 AN: 67960

Other (OTH) AF: 0.453 AC: 955 AN: 2110

Alfa AF: 0.465 Hom.: 28660

Bravo AF: 0.475

Asia WGS AF: 0.401 AC: 1393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.43
PhyloP100		0.0040
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: rs2544165; hg19: chr7-133920443;