NM_000375.3:c.-26-177T>C

Variant names:

• chr10-125816702-A-G
• rs397515348
• NM_000375.3:c.-26-177T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_000375.3(UROS):​c.-26-177T>C variant causes a intron change. The variant allele was found at a frequency of 0.00000202 in 494,254 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000020 (0 hom.)
• Consequence: UROS NM_000375.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.75
• Publications: 1 publications found

Genes affected

UROS (HGNC:12592): (uroporphyrinogen III synthase) The protein encoded by this gene catalyzes the fourth step of porphyrin biosynthesis in the heme biosynthetic pathway. Defects in this gene cause congenital erythropoietic porphyria (Gunther's disease). [provided by RefSeq, Jul 2008]

UROS Gene-Disease associations (from GenCC):

• cutaneous porphyria

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000375.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UROS	NM_000375.3	MANE Select	c.-26-177T>C		intron	N/A	NP_000366.1	A0A0S2Z4T8
	UROS	NM_001324036.2		c.-26-177T>C		intron	N/A	NP_001310965.1	A0A3B3ISM6
	UROS	NM_001324037.2		c.-26-177T>C		intron	N/A	NP_001310966.1	A0A3B3ITJ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UROS	ENST00000368797.10	TSL:1 MANE Select	c.-26-177T>C		intron	N/A	ENSP00000357787.4	P10746
	UROS	ENST00000940865.1		c.-26-177T>C		intron	N/A	ENSP00000610924.1
	UROS	ENST00000879953.1		c.-26-177T>C		intron	N/A	ENSP00000550012.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000202 AC: 1 AN: 494254 Hom.: 0 AF XY: 0.00000381 AC XY: 1 AN XY: 262588

African (AFR) AF: 0.00 AC: 0 AN: 13654

American (AMR) AF: 0.00 AC: 0 AN: 25594

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15382

East Asian (EAS) AF: 0.00 AC: 0 AN: 31488

South Asian (SAS) AF: 0.0000200 AC: 1 AN: 49960

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2230

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 297522

Other (OTH) AF: 0.00 AC: 0 AN: 27820

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	20
DANN	Benign	0.95
PhyloP100		4.7
PromoterAI		-0.18	Neutral
Mutation Taster		=3/97	disease causing

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: rs397515348; hg19: chr10-127505271;