rs1901216

Variant names:

• chr7-134238095-A-G
• rs1901216
• NM_144648.3:c.1984-9461A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-134238095-A-G
• chr7-134238095-A-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.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
• Publications: 0 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=-0.9).
• 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 rank	MANE	Protein	UniProt
LRGUK	NM_144648.3	c.1984-9461A>G		intron_variant	Intron 16 of 19	ENST00000285928.3	NP_653249.1
LRGUK	XM_024446659.2	c.1984-9461A>G		intron_variant	Intron 16 of 19		XP_024302427.1
LRGUK	XM_024446661.2	c.1984-9461A>G		intron_variant	Intron 16 of 19		XP_024302429.1
LRGUK	XM_047419890.1	c.1777-9461A>G		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.1984-9461A>G		intron_variant	Intron 16 of 19	1	NM_144648.3	ENSP00000285928.2

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

African (AFR) AF: 0.200 AC: 8317 AN: 41496

American (AMR) AF: 0.0513 AC: 785 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3470

East Asian (EAS) AF: 0.147 AC: 760 AN: 5180

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4828

European-Finnish (FIN) AF: 0.0110 AC: 117 AN: 10624

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00598 AC: 407 AN: 68026

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

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
PhyloP100		0.66
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: rs1901216; hg19: chr7-133922847;