5-26927958-T-C

Variant names:

• chr5-26927958-T-C
• rs10057565
• NM_016279.4:c.229-12034A>G

Variant summary

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

The NM_016279.4(CDH9):​c.229-12034A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,062 control chromosomes in the GnomAD database, including 872 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 0.096 (872 hom., cov: 32)
• Consequence: CDH9 NM_016279.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 4 publications found

Genes affected

CDH9 (HGNC:1768): (cadherin 9) This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. [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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016279.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH9	NM_016279.4	MANE Select	c.229-12034A>G		intron	N/A	NP_057363.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH9	ENST00000231021.9	TSL:1 MANE Select	c.229-12034A>G		intron	N/A	ENSP00000231021.4
	CDH9	ENST00000505045.1	TSL:1	n.402-12034A>G		intron	N/A
	CDH9	ENST00000513289.5	TSL:3	c.229-12034A>G		intron	N/A	ENSP00000426239.1

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14537 AN: 151944 Hom.: 870 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0957 AC: 14546 AN: 152062 Hom.: 872 Cov.: 32 AF XY: 0.0948 AC XY: 7046 AN XY: 74348

African (AFR) AF: 0.165 AC: 6860 AN: 41492

American (AMR) AF: 0.0701 AC: 1068 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3464

East Asian (EAS) AF: 0.174 AC: 899 AN: 5166

South Asian (SAS) AF: 0.121 AC: 584 AN: 4822

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10618

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0637 AC: 4331 AN: 67950

Other (OTH) AF: 0.0873 AC: 184 AN: 2108

Alfa AF: 0.0861 Hom.: 88

Bravo AF: 0.0995

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.42
PhyloP100		-0.97
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: rs10057565; hg19: chr5-26928066;