rs5762311

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CPMER (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CPMER	NR_186699.1	n.324+3382C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CPMER	ENST00000440255.1	n.324+3382C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.0636

Gnomad4 NFE AF: 0.0736

Gnomad4 OTH AF: 0.194

Alfa AF: 0.109 Hom.: 3577

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5762311; hg19: chr22-28090207;