rs6885387

Variant names:

• chr5-26939070-G-A
• rs6885387
• NM_016279.4:c.229-23146C>T

Variant summary

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

The NM_016279.4(CDH9):​c.229-23146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,612 control chromosomes in the GnomAD database, including 25,094 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 0.57 (25094 hom., cov: 32)
• Consequence: CDH9 NM_016279.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH9	NM_016279.4	MANE Select	c.229-23146C>T		intron	N/A	NP_057363.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDH9	ENST00000231021.9	TSL:1 MANE Select	c.229-23146C>T		intron	N/A	ENSP00000231021.4	Q9ULB4
	CDH9	ENST00000505045.1	TSL:1	n.402-23146C>T		intron	N/A
	CDH9	ENST00000513289.5	TSL:3	c.229-23146C>T		intron	N/A	ENSP00000426239.1	E7EPN0

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86503 AN: 151494 Hom.: 25069 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.571 AC: 86572 AN: 151612 Hom.: 25094 Cov.: 32 AF XY: 0.565 AC XY: 41859 AN XY: 74044

African (AFR) AF: 0.605 AC: 25050 AN: 41438

American (AMR) AF: 0.454 AC: 6923 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2287 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1894 AN: 5140

South Asian (SAS) AF: 0.349 AC: 1673 AN: 4798

European-Finnish (FIN) AF: 0.641 AC: 6709 AN: 10470

Middle Eastern (MID) AF: 0.523 AC: 136 AN: 260

European-Non Finnish (NFE) AF: 0.594 AC: 40233 AN: 67786

Other (OTH) AF: 0.559 AC: 1174 AN: 2102

Alfa AF: 0.583 Hom.: 36419

Bravo AF: 0.558

Asia WGS AF: 0.351 AC: 1205 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.38
PhyloP100		-0.48
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: rs6885387; hg19: chr5-26939178;