16-64947363-GT-GTTTTT

Variant names:

• chr16-64947363-G-GTTTT
• rs34181449
• NM_001797.4:c.*236_*239dupAAAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001797.4(CDH11):​c.*236_*239dupAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH11	NM_001797.4	c.*236_*239dupAAAA		3_prime_UTR_variant	Exon 13 of 13	ENST00000268603.9	NP_001788.2
CDH11	NM_001308392.2	c.*724_*727dupAAAA		3_prime_UTR_variant	Exon 14 of 14		NP_001295321.1
CDH11	NM_001330576.2	c.*236_*239dupAAAA		3_prime_UTR_variant	Exon 12 of 12		NP_001317505.1
CDH11	XM_047433486.1	c.*236_*239dupAAAA		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.*236_*239dupAAAA		3_prime_UTR_variant	Exon 13 of 13	1	NM_001797.4	ENSP00000268603.4
CDH11	ENST00000394156	c.*724_*727dupAAAA		3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000377711.3
CDH11	ENST00000566827.5	c.*236_*239dupAAAA		downstream_gene_variant		2		ENSP00000457812.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1000576 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 474998

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;