rs9608641

chr22-27697714-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000440255.1(CPMER):n.214-13C>T variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,048 control chromosomes in the GnomAD database, including 9,636 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 0.33 (9634 hom., cov: 32)
  • Exomes 𝑓: 0.50 (2 hom.)
• Consequence: CPMER ENST00000440255.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

CPMER (HGNC:55992): (cytoplasmic mesoderm regulator)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPMER	ENST00000440255.1	n.214-13C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50631 AN: 151918 Hom.: 9637 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.355

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 2 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.333 AC: 50654 AN: 152038 Hom.: 9634 Cov.: 32 AF XY: 0.333 AC XY: 24745 AN XY: 74296

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.0878

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.353

Alfa AF: 0.406 Hom.: 13349

Bravo AF: 0.318

Asia WGS AF: 0.284 AC: 991 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	0.12
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9608641; hg19: chr22-28093712;