rs34181449

Variant names:

• chr16-64947363-GT-G
• rs34181449
• ENST00000268603:c.*239delA

Your query was ambiguous. Multiple possible variants found:

• chr16-64947363-GT-G
• chr16-64947363-GT-GTT
• chr16-64947363-GT-GTTT
• chr16-64947363-GT-GTTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001797.4(CDH11):​c.*239delA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0537 in 1,147,584 control chromosomes in the GnomAD database, including 1,421 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.039 (122 hom., cov: 32)
  • Exomes 𝑓: 0.056 (1299 hom.)
• Consequence: CDH11 NM_001797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

Genes affected

CDH11 (HGNC:1750): (cadherin 11) 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. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Expression of this particular cadherin in osteoblastic cell lines, and its upregulation during differentiation, suggests a specific function in bone development and maintenance. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.051 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH11	NM_001797.4	c.*239delA		3_prime_UTR_variant	Exon 13 of 13	ENST00000268603.9	NP_001788.2
CDH11	NM_001308392.2	c.*727delA		3_prime_UTR_variant	Exon 14 of 14		NP_001295321.1
CDH11	NM_001330576.2	c.*239delA		3_prime_UTR_variant	Exon 12 of 12		NP_001317505.1
CDH11	XM_047433486.1	c.*239delA		3_prime_UTR_variant	Exon 12 of 12		XP_047289442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH11	ENST00000268603	c.*239delA		3_prime_UTR_variant	Exon 13 of 13	1	NM_001797.4	ENSP00000268603.4
CDH11	ENST00000394156	c.*727delA		3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000377711.3
CDH11	ENST00000566827.5	c.*239delA		downstream_gene_variant		2		ENSP00000457812.1

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5759 AN: 148034 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.0189

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0342

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.0436

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0196

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0374

GnomAD4 exome AF: 0.0559 AC: 55870 AN: 999466 Hom.: 1299 Cov.: 27 AF XY: 0.0556 AC XY: 26381 AN XY: 474460

Gnomad4 AFR exome AF: 0.0204

Gnomad4 AMR exome AF: 0.0278

Gnomad4 ASJ exome AF: 0.0400

Gnomad4 EAS exome AF: 0.0109

Gnomad4 SAS exome AF: 0.0402

Gnomad4 FIN exome AF: 0.0474

Gnomad4 NFE exome AF: 0.0597

Gnomad4 OTH exome AF: 0.0515

GnomAD4 genome AF: 0.0389 AC: 5759 AN: 148118 Hom.: 122 Cov.: 32 AF XY: 0.0384 AC XY: 2771 AN XY: 72184

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.0342

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0430

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.0365

Alfa AF: 0.0134 Hom.: 5

Bravo AF: 0.0354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34181449; hg19: chr16-64981266;