rs10232743

Variant names:

• chr7-43871283-C-T
• rs10232743
• ENST00000603700.1:c.176-1907G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000603700.1(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 ENST00000603700.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 55 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901620	XR_007060296.1	n.1525C>T		non_coding_transcript_exon_variant	Exon 2 of 2
URGCP-MRPS24	NM_001204871.2	c.176-1907G>A		intron_variant	Intron 4 of 6		NP_001191800.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
URGCP-MRPS24	ENST00000603700.1	c.176-1907G>A		intron_variant	Intron 4 of 6	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

African (AFR) AF: 0.00433 AC: 180 AN: 41578

American (AMR) AF: 0.0136 AC: 208 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.00622 AC: 30 AN: 4824

European-Finnish (FIN) AF: 0.0548 AC: 582 AN: 10614

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

European-Non Finnish (NFE) AF: 0.0297 AC: 2020 AN: 68022

Other (OTH) AF: 0.0170 AC: 36 AN: 2116

Alfa AF: 0.0197 Hom.: 29

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism

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: rs10232743; hg19: chr7-43910882;