rs3915737

chr20-46242742-A-Cchr20-46242742-A-Gchr20-46242742-A-T

Variant summary

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

The NM_021248.3(CDH22):c.256-1485T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,970 control chromosomes in the GnomAD database, including 7,052 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 0.30 (7052 hom., cov: 32)
• Consequence: CDH22 NM_021248.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDH22	NM_021248.3	c.256-1485T>G		intron_variant		ENST00000537909.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDH22	ENST00000537909.4	c.256-1485T>G		intron_variant		2	NM_021248.3	P1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45268 AN: 151852 Hom.: 7047 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.298 AC: 45298 AN: 151970 Hom.: 7052 Cov.: 32 AF XY: 0.299 AC XY: 22185 AN XY: 74274

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.284

Alfa AF: 0.229 Hom.: 1315

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.098
Dann	Benign	0.59

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

Publications

LitVar

Other links and lift over

dbSNP: rs3915737; hg19: chr20-44871381;