rs2272040

Variant names:

• chr4-70141330-A-G
• rs2272040
• ENST00000502441.2:n.98-62A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502441.2(PRR27):​n.98-62A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 400,876 control chromosomes in the GnomAD database, including 3,858 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 0.12 (1269 hom., cov: 32)
  • Exomes 𝑓: 0.14 (2589 hom.)
• Consequence: PRR27 ENST00000502441.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 4 publications found

Genes affected

PRR27 (HGNC:33193): (proline rich 27) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CSN1S2BP (HGNC:20227): (casein alpha s2 like B, pseudogene) This locus is found in a cluster of casein genes, similar to other mammals. In human, the potential open reading frame that matches the homologous protein from other species is prematurely truncated shortly after the signal peptide. Therefore, this locus appears to be a pseudogene. [provided by RefSeq, Feb 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSN1S2BP	NR_033311.1	n.110-62A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRR27	ENST00000502441.2	n.98-62A>G		intron_variant	Intron 3 of 10	3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17673 AN: 151972 Hom.: 1268 Cov.: 32

Gnomad AFR AF: 0.0464

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0852

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.139 AC: 34459 AN: 248786 Hom.: 2589 AF XY: 0.140 AC XY: 20119 AN XY: 143768

African (AFR) AF: 0.0450 AC: 265 AN: 5886

American (AMR) AF: 0.170 AC: 2401 AN: 14140

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 1594 AN: 7494

East Asian (EAS) AF: 0.197 AC: 1746 AN: 8862

South Asian (SAS) AF: 0.143 AC: 6945 AN: 48490

European-Finnish (FIN) AF: 0.0830 AC: 873 AN: 10516

Middle Eastern (MID) AF: 0.185 AC: 165 AN: 894

European-Non Finnish (NFE) AF: 0.134 AC: 18834 AN: 140850

Other (OTH) AF: 0.140 AC: 1636 AN: 11654

GnomAD4 genome AF: 0.116 AC: 17678 AN: 152090 Hom.: 1269 Cov.: 32 AF XY: 0.116 AC XY: 8647 AN XY: 74348

African (AFR) AF: 0.0463 AC: 1922 AN: 41518

American (AMR) AF: 0.173 AC: 2637 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1008 AN: 5170

South Asian (SAS) AF: 0.138 AC: 664 AN: 4822

European-Finnish (FIN) AF: 0.0852 AC: 900 AN: 10558

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9291 AN: 67976

Other (OTH) AF: 0.166 AC: 350 AN: 2108

Alfa AF: 0.133 Hom.: 733

Bravo AF: 0.122

Asia WGS AF: 0.140 AC: 485 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0090
DANN	Benign	0.41
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs2272040; hg19: chr4-71007047;