chr16-64973909-C-T

Variant names:

• chr16-64973909-C-T
• rs973200
• NM_001797.4:c.1254-869G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001797.4(CDH11):​c.1254-869G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,960 control chromosomes in the GnomAD database, including 16,734 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 0.46 (16734 hom., cov: 32)
• Consequence: CDH11 NM_001797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH11	NM_001797.4	c.1254-869G>A		intron_variant	Intron 8 of 12	ENST00000268603.9	NP_001788.2
CDH11	NM_001308392.2	c.1254-869G>A		intron_variant	Intron 8 of 13		NP_001295321.1
CDH11	NM_001330576.2	c.876-869G>A		intron_variant	Intron 7 of 11		NP_001317505.1
CDH11	XM_047433486.1	c.876-869G>A		intron_variant	Intron 7 of 11		XP_047289442.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH11	ENST00000268603.9	c.1254-869G>A		intron_variant	Intron 8 of 12	1	NM_001797.4	ENSP00000268603.4
CDH11	ENST00000394156.7	c.1254-869G>A		intron_variant	Intron 8 of 13	1		ENSP00000377711.3
CDH11	ENST00000566827.5	c.876-869G>A		intron_variant	Intron 7 of 11	2		ENSP00000457812.1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69217 AN: 151842 Hom.: 16721 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.456 AC: 69259 AN: 151960 Hom.: 16734 Cov.: 32 AF XY: 0.469 AC XY: 34811 AN XY: 74266

Gnomad4 AFR AF: 0.325

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.480

Alfa AF: 0.451 Hom.: 2398

Bravo AF: 0.448

Asia WGS AF: 0.717 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.39

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: rs973200; hg19: chr16-65007812;