rs3915737

Variant names:

• chr20-46242742-A-C
• rs3915737
• NM_021248.3:c.256-1485T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-46242742-A-C
• chr20-46242742-A-G
• chr20-46242742-A-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.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
• Publications: 3 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=-0.92).
• 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 rank	MANE	Protein	UniProt
CDH22	NM_021248.3	c.256-1485T>G		intron_variant	Intron 2 of 11	ENST00000537909.4	NP_067071.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH22	ENST00000537909.4	c.256-1485T>G		intron_variant	Intron 2 of 11	2	NM_021248.3	ENSP00000437790.1

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

African (AFR) AF: 0.397 AC: 16458 AN: 41414

American (AMR) AF: 0.267 AC: 4085 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3472

East Asian (EAS) AF: 0.291 AC: 1503 AN: 5160

South Asian (SAS) AF: 0.237 AC: 1142 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3544 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16812 AN: 67946

Other (OTH) AF: 0.284 AC: 601 AN: 2114

Alfa AF: 0.245 Hom.: 1884

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
PhyloP100		-0.95
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: rs3915737; hg19: chr20-44871381;