rs1044930098

Variant names:

• chrX-134460332-C-A
• rs1044930098
• NM_000194.3:c.21C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-134460332-C-A
• chrX-134460332-C-T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_000194.3(HPRT1):​c.21C>A​(p.Gly7Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000008 in 1,124,829 control chromosomes in the GnomAD database, including 1 homozygotes. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G7G) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000044 (1 hom., 2 hem., cov: 24)
  • Exomes 𝑓: 0.0000040 (0 hom. 1 hem.)
• Consequence: HPRT1 NM_000194.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.584

Genes affected

HPRT1 (HGNC:5157): (hypoxanthine phosphoribosyltransferase 1) The protein encoded by this gene is a transferase, which catalyzes conversion of hypoxanthine to inosine monophosphate and guanine to guanosine monophosphate via transfer of the 5-phosphoribosyl group from 5-phosphoribosyl 1-pyrophosphate. This enzyme plays a central role in the generation of purine nucleotides through the purine salvage pathway. Mutations in this gene result in Lesch-Nyhan syndrome or gout.[provided by RefSeq, Jun 2009]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BP6: Variant X-134460332-C-A is Benign according to our data. Variant chrX-134460332-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2928796.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.584 with no splicing effect.
• BS2: High Hemizygotes in GnomAd4 at 2 XLR,XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HPRT1	NM_000194.3	c.21C>A	p.Gly7Gly	synonymous_variant	Exon 1 of 9	ENST00000298556.8	NP_000185.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HPRT1	ENST00000298556.8	c.21C>A	p.Gly7Gly	synonymous_variant	Exon 1 of 9	1	NM_000194.3	ENSP00000298556.7
HPRT1	ENST00000462974.5	n.-19C>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0000442 AC: 5 AN: 113097 Hom.: 1 Cov.: 24

Gnomad AFR AF: 0.000160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000124 AC: 1 AN: 80921 AF XY: 0.00

Gnomad AFR exome AF: 0.000400

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000395 AC: 4 AN: 1011732 Hom.: 0 Cov.: 29 AF XY: 0.00000306 AC XY: 1 AN XY: 326482

African (AFR) AF: 0.000183 AC: 4 AN: 21898

American (AMR) AF: 0.00 AC: 0 AN: 26639

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17348

East Asian (EAS) AF: 0.00 AC: 0 AN: 23624

South Asian (SAS) AF: 0.00 AC: 0 AN: 47952

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 25463

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2974

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 803564

Other (OTH) AF: 0.00 AC: 0 AN: 42270

GnomAD4 genome AF: 0.0000442 AC: 5 AN: 113097 Hom.: 1 Cov.: 24 AF XY: 0.0000565 AC XY: 2 AN XY: 35401

African (AFR) AF: 0.000160 AC: 5 AN: 31284

American (AMR) AF: 0.00 AC: 0 AN: 10831

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2657

East Asian (EAS) AF: 0.00 AC: 0 AN: 3550

South Asian (SAS) AF: 0.00 AC: 0 AN: 2858

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6200

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 237

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53271

Other (OTH) AF: 0.00 AC: 0 AN: 1529

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Lesch-Nyhan syndrome;C0268117:Partial hypoxanthine-guanine phosphoribosyltransferase deficiency Benign:1

Jul 16, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	14
DANN	Benign	0.93
PhyloP100		0.58
PromoterAI		0.018	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Other links and lift over

dbSNP: rs1044930098; hg19: chrX-133594362;