rs1450890

Variant names:

• chr7-134249445-G-A
• rs1450890
• NM_144648.3:c.2198+369G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-134249445-G-A
• chr7-134249445-G-C
• chr7-134249445-G-T

Variant summary

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

The NM_144648.3(LRGUK):​c.2198+369G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,016 control chromosomes in the GnomAD database, including 4,955 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 (4955 hom., cov: 32)
• Consequence: LRGUK NM_144648.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144648.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRGUK	NM_144648.3	MANE Select	c.2198+369G>A		intron	N/A	NP_653249.1	Q96M69

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRGUK	ENST00000285928.3	TSL:1 MANE Select	c.2198+369G>A		intron	N/A	ENSP00000285928.2	Q96M69

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35233 AN: 151898 Hom.: 4951 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.232 AC: 35237 AN: 152016 Hom.: 4955 Cov.: 32 AF XY: 0.233 AC XY: 17272 AN XY: 74288

African (AFR) AF: 0.108 AC: 4499 AN: 41474

American (AMR) AF: 0.189 AC: 2891 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3472

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5174

South Asian (SAS) AF: 0.151 AC: 726 AN: 4814

European-Finnish (FIN) AF: 0.408 AC: 4303 AN: 10556

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20795 AN: 67942

Other (OTH) AF: 0.247 AC: 522 AN: 2112

Alfa AF: 0.269 Hom.: 5143

Bravo AF: 0.210

Asia WGS AF: 0.129 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.54
PhyloP100		-0.61
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: rs1450890; hg19: chr7-133934197;