20-46231832-C-A

Variant names:

• chr20-46231832-C-A
• rs2050113
• NM_021248.3:c.551-4205G>T

Variant summary

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

The NM_021248.3(CDH22):​c.551-4205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,166 control chromosomes in the GnomAD database, including 59,541 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 0.88 (59541 hom., cov: 32)
• Consequence: CDH22 NM_021248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 6 publications found

Genes affected

CDH22 (HGNC:13251): (cadherin 22) This gene is a member of the cadherin superfamily. The gene product is composed of five cadherin repeat domains and a cytoplasmic tail similar to the highly conserved cytoplasmic region of classical cadherins. Expressed predominantly in the brain, this putative calcium-dependent cell adhesion protein may play an important role in morphogenesis and tissue formation in neural and non-neural cells during development and maintenance of the brain and neuroendocrine organs. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH22	NM_021248.3	c.551-4205G>T		intron_variant	Intron 3 of 11	ENST00000537909.4	NP_067071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH22	ENST00000537909.4	c.551-4205G>T		intron_variant	Intron 3 of 11	2	NM_021248.3	ENSP00000437790.1

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134183 AN: 152048 Hom.: 59497 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.882 AC: 134282 AN: 152166 Hom.: 59541 Cov.: 32 AF XY: 0.879 AC XY: 65411 AN XY: 74390

African (AFR) AF: 0.830 AC: 34444 AN: 41492

American (AMR) AF: 0.840 AC: 12843 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3188 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3670 AN: 5162

South Asian (SAS) AF: 0.864 AC: 4162 AN: 4816

European-Finnish (FIN) AF: 0.933 AC: 9902 AN: 10618

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63134 AN: 67994

Other (OTH) AF: 0.893 AC: 1887 AN: 2114

Alfa AF: 0.910 Hom.: 273161

Bravo AF: 0.872

Asia WGS AF: 0.803 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.40
DANN	Benign	0.23
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs2050113; hg19: chr20-44860471;