rs2045184

Variant names:

• chr10-124526735-C-G
• rs2045184
• NM_022126.4:c.716+9464C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-124526735-C-G
• chr10-124526735-C-T

Variant summary

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

The NM_022126.4(LHPP):​c.716+9464C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,126 control chromosomes in the GnomAD database, including 8,302 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 0.31 (8302 hom., cov: 32)
• Consequence: LHPP NM_022126.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 1 publications found

Genes affected

LHPP (HGNC:30042): (phospholysine phosphohistidine inorganic pyrophosphate phosphatase) Enables inorganic diphosphatase activity and protein homodimerization activity. Involved in phosphate-containing compound metabolic process. Located in cytosol and nuclear speck. [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 (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LHPP	NM_022126.4	c.716+9464C>G		intron_variant	Intron 6 of 6	ENST00000368842.10	NP_071409.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LHPP	ENST00000368842.10	c.716+9464C>G		intron_variant	Intron 6 of 6	1	NM_022126.4	ENSP00000357835.5
LHPP	ENST00000368839.1	c.624+28607C>G		intron_variant	Intron 5 of 5	1		ENSP00000357832.1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47824 AN: 152008 Hom.: 8293 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.315 AC: 47847 AN: 152126 Hom.: 8302 Cov.: 32 AF XY: 0.310 AC XY: 23086 AN XY: 74364

African (AFR) AF: 0.171 AC: 7121 AN: 41524

American (AMR) AF: 0.378 AC: 5784 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1182 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1795 AN: 5162

South Asian (SAS) AF: 0.221 AC: 1064 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3046 AN: 10570

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26603 AN: 67970

Other (OTH) AF: 0.334 AC: 705 AN: 2112

Alfa AF: 0.349 Hom.: 1232

Bravo AF: 0.316

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.056
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: rs2045184; hg19: chr10-126215304;