rs5762311

Variant names:

• chr22-27694209-G-A
• rs5762311
• ENST00000440255.1:n.324+3382C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-27694209-G-A
• chr22-27694209-G-C

Variant summary

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

The ENST00000440255.1(CPMER):​n.324+3382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,120 control chromosomes in the GnomAD database, including 4,257 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 0.19 (4257 hom., cov: 32)
• Consequence: CPMER ENST00000440255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779
• Publications: 13 publications found

Genes affected

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

ENSG00000295854 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CPMER	NR_186699.1	n.324+3382C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CPMER	ENST00000440255.1	n.324+3382C>T		intron_variant	Intron 3 of 4	3
ENSG00000295854	ENST00000733137.1	n.392-18002C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28701 AN: 152002 Hom.: 4251 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.0636

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0736

Gnomad OTH AF: 0.191

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.189 AC: 28730 AN: 152120 Hom.: 4257 Cov.: 32 AF XY: 0.192 AC XY: 14248 AN XY: 74360

African (AFR) AF: 0.327 AC: 13551 AN: 41494

American (AMR) AF: 0.255 AC: 3902 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3472

East Asian (EAS) AF: 0.621 AC: 3212 AN: 5170

South Asian (SAS) AF: 0.271 AC: 1305 AN: 4820

European-Finnish (FIN) AF: 0.0636 AC: 673 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0736 AC: 5004 AN: 67994

Other (OTH) AF: 0.194 AC: 409 AN: 2110

Alfa AF: 0.126 Hom.: 7584

Bravo AF: 0.211

Asia WGS AF: 0.391 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.57
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs5762311; hg19: chr22-28090207;