rs10232743

Positions:

• chr7-43871283-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001204871.2(URGCP-MRPS24):​c.176-1907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 152,320 control chromosomes in the GnomAD database, including 55 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 0.020 (55 hom., cov: 33)
• Consequence: URGCP-MRPS24 NM_001204871.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

Genes affected

URGCP-MRPS24 (HGNC:49188): (URGCP-MRPS24 readthrough) This locus represents naturally occurring read-through transcription between the neighboring URGCP (upregulator of cell proliferation) and MRPS24 (mitochondrial ribosomal protein S24) genes on chromosome 7. The read-through transcript is predicted to encode a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to a frameshift relative to the downstream gene. [provided by RefSeq, Mar 2011]

LOC124901620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0204 (3113/152320) while in subpopulation NFE AF= 0.0297 (2020/68022). AF 95% confidence interval is 0.0286. There are 55 homozygotes in gnomad4. There are 1586 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 55 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
URGCP-MRPS24	NM_001204871.2	c.176-1907G>A		intron_variant			NP_001191800.1
LOC124901620	XR_007060296.1	n.1525C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
URGCP-MRPS24	ENST00000603700.1	c.176-1907G>A		intron_variant		5		ENSP00000473871.1

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3115 AN: 152202 Hom.: 55 Cov.: 33

Gnomad AFR AF: 0.00434

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0136

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00621

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.0172

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

GnomAD4 genome AF: 0.0204 AC: 3113 AN: 152320 Hom.: 55 Cov.: 33 AF XY: 0.0213 AC XY: 1586 AN XY: 74472

Gnomad4 AFR AF: 0.00433

Gnomad4 AMR AF: 0.0136

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00622

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.0170

Alfa AF: 0.0258 Hom.: 20

Bravo AF: 0.0163

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs10232743; hg19: chr7-43910882;