rs2074503

Variant names:

• chr6-30562719-T-A
• rs2074503
• NM_025263.4:c.*224T>A

Your query was ambiguous. Multiple possible variants found:

• chr6-30562719-T-A
• chr6-30562719-T-C
• chr6-30562719-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_025263.4(PRR3):​c.*224T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PRR3 NM_025263.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 27 publications found

Genes affected

PRR3 (HGNC:21149): (proline rich 3) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000290047 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025263.4. 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
	PRR3	NM_025263.4	MANE Select	c.*224T>A		3_prime_UTR	Exon 4 of 4	NP_079539.2
	PRR3	NM_001077497.3		c.*224T>A		3_prime_UTR	Exon 3 of 3	NP_001070965.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR3	ENST00000376560.8	TSL:1 MANE Select	c.*224T>A		3_prime_UTR	Exon 4 of 4	ENSP00000365744.4
	PRR3	ENST00000376557.3	TSL:2	c.*224T>A		3_prime_UTR	Exon 3 of 3	ENSP00000365740.3
	PRR3	ENST00000934408.1		c.*224T>A		3_prime_UTR	Exon 2 of 2	ENSP00000604467.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 266492 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 137042

African (AFR) AF: 0.00 AC: 0 AN: 7474

American (AMR) AF: 0.00 AC: 0 AN: 9104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9220

East Asian (EAS) AF: 0.00 AC: 0 AN: 22896

South Asian (SAS) AF: 0.00 AC: 0 AN: 10658

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21230

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 167646

Other (OTH) AF: 0.00 AC: 0 AN: 16948

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.87
DANN	Benign	0.43
PhyloP100		-2.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2074503; hg19: chr6-30530496;